Biology subjects

Girard, M.

Publications and source records attributed to Girard, M..

At least 19 recordsLinked to original sources

bioRxiv2026

Multi-Chain Hamiltonian Replica Exchange Framework for Probing Transient Helices and Order-Disorder Transitions in Proteins

Simulations have emerged as a pillar in biophysics to understand behavior at the molecular scale, in particular for proteins such as intrinsically disordered proteins. These often show transient folding with long-lived states that are challenging to efficiently sample using conventional simulations. Here, we show that Hamiltonian replica-exchange at the level of hydrogen bonds can be used to systematically explore the conformational landscape of proteins. Investigating the IM30 protein, a partially alpha helical protein, under the PLUM coarse-grain force-field, we show that this approach straightforwardly allows characterization of local helix stability, which would be otherwise hard to obtain. For instance, we show that some regions of the conserved coiled-coil structure are less stable than others. By combining the different replicas with principal component analysis, we are able to dissect the conformational landscape of the IM30 protein. Taken together, this indicates that enhanced sampling remains an important part of simulations, allowing insights that cannot be easily obtained in traditional simulations.

biophysics↗

bioRxiv2026

A Phosphorylation-Induced Micellization switch in the low complexity domain of TDP-43

Abstract textPhase separation (PS) of the low-complexity domain (LCD) of TDP-43 is linked to pathogenic aggregates in amyotrophic lateral sclerosis (ALS) and frontotemporal lobar degeneration (FTLD-TDP). Here, we show that extensive phosphorylation of the LCD C-terminus redirects its self-assembly. Coarse-grained Monte Carlo simulations predicted that 12 Ser phosphorylations partition the 148-residue LCD into a hydrophobic N-terminal and highly charged C-terminal block, favoring finite-sized micellization over macroscopic PS. In vitro, LCD phosphorylated by casein kinase 1 delta (CK1{delta}; mean of 12 phosphorylations by native mass spectrometry) and phosphomimetic 12D/12DD mutants formed spherical nanoparticles ({approx} 20-50 nm) above a low-micromolar critical micelle concentration, whereas the unphosphorylated LCD underwent reversible PS that matured into fibrils. Increasing ionic strength shifted the mutants toward anisotropic morphologies (worm-like 12D micelles and rigid 12DD nanocylinders). Turbidity assays and confocal imaging directly visualized the absence of PS in the phosphorylated form. Negative-stain and cryo-EM confirmed the spherical micellar architecture for the phosphorylated LCD and 12D/12DD mimics. Our data identify phosphorylation as a molecular switch tuning macrophase separation and fibril formation of TDP-43 LCD, providing a framework for an aggregation-protective role through microphase separation into size-limited micelles. Whether these assemblies are stable or kinetically trapped on pathological timescales remains unclear.

biophysics↗

bioRxiv2026

Pitx2-associated early-onset glaucoma alters corneal innervation and sensory function in a sex-specific manner

PurposePitx2-associated developmental glaucoma is characterized by anterior segment dysgenesis, ocular hypertension, and optic neuropathy. Its consequences for corneal sensory innervation remain poorly understood. We investigated whether this disease alters corneal nerve structure and sensory function in a sex-dependent manner. MethodsMale and female Pitx2egl1/egl1 and Pitx2+/+ mice were examined at 1 and 3 months. Ocular phenotyping included intraocular pressure, fundus imaging, visual evoked potentials, and optic nerve ultrastructure. RNA sequencing of corneas and trigeminal ganglia was performed at 3 months. Corneal innervation was assessed by {beta}III-tubulin immunofluorescence and volumetric quantification of nerve fibers. Corneal sensitivity was measured using Von Frey filaments. ResultsPitx2egl1/egl1 mice developed progressive ocular hypertension, fundus abnormalities, reduced visual evoked potential amplitudes, and optic nerve degeneration, supporting the model as early-onset glaucoma. Baseline sex-related transcriptional differences were limited in both cornea and trigeminal ganglia. In contrast, Pitx2 mutation induced sex-dependent molecular responses. Female corneas showed broader transcriptional changes enriched in inflammatory, stress-response, and tissue-remodeling pathways, whereas male corneas showed a more restricted response involving metabolic and homeostatic processes. Similar sex divergence was observed in trigeminal ganglia. Corneal nerve fiber volume was reduced in both sexes at 3 months but not at 1 month, whereas reduced sensitivity was detected only in mutant males. ConclusionsThis study identifies sexual dimorphism as a component of Pitx2-associated developmental glaucoma. Furthermore, our findings suggest that glaucoma affects the corneal sensory system beyond optic nerve pathology, highlighting a potentially overlooked dimension of disease relevant to ocular surface monitoring and patient management. HighlightsO_LIDisruption of the cornea-trigeminal ganglion axis with coordinated molecular and functional alterations in Pitx2-associated early-onset glaucoma C_LIO_LISex-dependent modifications in both cornea and trigeminal ganglion responses to early-onset glaucoma C_LIO_LIProgressive corneal neurodegeneration in early-onset glaucoma C_LI

neuroscience↗

bioRxiv2026

The structured hairpin region of the bacterial ESCRT-III protein IM30 orchestrates stress-induced condensate formation

Biomolecular condensates are well characterized in eukaryotes, but their role in bacteria remains largely elusive. In the cyanobacteriumn Synechocystis sp. PCC 6803, the protein IM30, a member of the ESCRT-III superfamily of membrane remodeling proteins, forms stress-induced puncta across diverse environmental challenges, indicating a general adaptive response. Live-cell imaging reveals that IM30 is uniformly distributed throughout the cytoplasm at low concentrations but assembles into puncta upon exceeding a critical saturation threshold, a hallmark of liquid-liquid phase separation. Crucially, stress triggers puncta formation even below this threshold, suggesting stress lowers the phase-separation barrier. Super-resolution microscopy confirms spherical, condensate-like morphologies, while FRAP demonstrates rapid fluorescence recovery, consistent with with a fluid interior and dynamic exchange between puncta and the cytosol. Cellular IM30 levels exceed the in vitro determined critical concentration, placing the protein in a supersaturated state primed for condensation. Domain mapping identifies the structured 1-3 helical hairpin as the minimal phase separation driver; in contrast, the disordered 4-6 segment alone cannot phase-separate. Phase separation occurs within a physiologically relevant pH range (4.5-6.5), matching the localized acidification of the cyanobacterial cytoplasm at damaged thylakoid membranes. This directly links membrane stress, pH changes, and IM30 recruitment. Collectively, these findings establish IM30 puncta as bona fide, stress-responsive biomolecular condensates that function as rapid stress sensors and effectors, providing a mechanistic framework for phase separation and condensate formation by bacterial ESCRT-III proteins during environmental adaptation.

biochemistry↗

bioRxiv2025

Physics of low complexity polymers: patterning, polymer collapse and bulk microphases

Polymer physics has arisen as a pillar of understanding behavior of intrinsically disordered proteins. Behavior of polymers can be understood in terms of generic behavior. Specifically, phase behavior can be understood in terms of solvent quality and chain length. The theory is well established for homopolymers, and specific heteropolymer structures, in particular random and co-block polymers. However, protein sequiences are neither of these. Nevertheless, there is a clear link between sequence and properties, which has given rise to the concept of molecular grammar. In this article, we establish a framework to understand the behavior of Sturmian polymers, which provide a reasonable non-random polymer model for disordered proteins. Specifically, we show that molecular grammar arises as a non-linear critical susceptibility near the{theta} transition of single chains. We demonstrate that molecular grammar exists in polymer melts, where is determines a length scale under which chains are compressed, and above which chains are expanded.

biophysics↗

bioRxiv2025

Compressed inverted indexes for scalable sequence similarity

Modern sequencing continues to drive explosive growth of nucleotide sequence archives, pushing MinHash sketching methods to their scalability limits. Tools such as Mash, Dashing2, and Bindash2 provide compact sketches and accurate similarity estimates, but they typically use forward indexes that materialize each sketch as an explicit fingerprint vector. This architecture makes large-scale similarity search and collection-versus-collection comparison costly in both time and memory, especially at the scale of millions of sequences. We revisit sketch index architectures and develop a framework based on inverted indexes over sketch fingerprints. We introduce a cost model for sketch comparison and prove that, with suitably compressed posting lists, inverted indexes can match the asymptotic space complexity of forward indexes. Using this model, we design all-vs-all comparison algorithms between two inverted indexes whose running time is proportional to the total number of matching sketch positions, yielding outputsensitive optimality and enabling efficient large collection comparisons at scale. Because many applications impose similarity thresholds, we add two early-pruning schemes for Jaccard similarity. The first is exact and eliminates pairs guaranteed not to reach a target threshold. The second is probabilistic and exploits partial match statistics to discard pairs unlikely to exceed the threshold, with explicit control of the false-rejection probability. These schemes reduce time and memory while preserving rigorous guarantees on retained high-similarity pairs. We implement these ideas in Onika, an open-source Rust system built on compressed inverted posting lists at github.com/Malfoy/Onika. Onika also applies similarity-aware document reordering to shrink index size and improve locality, especially for redundant collections. Experiments on bacterial genome repositories and long-read HiFi datasets show that Onika matches or improves sketch sizes of leading tools while accelerating large-scale search and collection-versus-collection comparison by up to several orders of magnitude in low-redundancy regimes, without compromising sensitivity at practically relevant similarity thresholds.

bioinformatics↗

bioRxiv2025

Reversible multiscale corneal sexual dimorphism orchestrates neuro-epithelial coupling and tear proteome composition

Donor-recipient sex mismatch is an under-recognized risk factor for corneal graft rejection, yet the biological underpinnings at the ocular surface remain undefined. We hypothesized that sex hormones coordinately tune the tear-nerve-epithelium axis and that androgen exposure could normalize sex-linked differences relevant to alloimmune risk. We profiled 12-week-old mice in three hormonal contexts, i.e. male, female, and testosterone-treated female, combining tear biochemistry and label-free proteomics with epithelial lineage dynamics, in vivo sensory function, and corneal/trigeminal transcriptional readouts. Tear collection rate was comparable across groups, but total tear protein was reduced in females. Proteomics revealed extensive sex differences in extracellular composition, spanning lipid transport, protease-antiprotease balance, complement activity, and secretory/mucin pathways. Epithelial analyses showed sex-linked differences in progenitor output and spatial deployment, and sensory metrics indicated divergent innervation architecture and function. Across modalities, androgen supplementation in females shifted molecular and physiological profiles toward the male state, attenuating nearly all dimorphic signals, demonstrating that close to all sexual dimorphism observed here is reversible by testosterone and reflects an actively maintained endocrine state rather than a fixed developmental program. Complementary metabolite profiling provides a sex-stratified atlas of free modified nucleosides in tears, positioning extracellular epitranscriptomic markers as accessible indicators of hormonal context. Together, these results establish a multiscale, hormone-responsive sexual dimorphism at the ocular surface and offer a mechanistic framework linking sex and endocrine status to parameters that influence graft integration. They motivate sex-aware biomarkers, stratification by hormonal context in diagnostics and trials, and therapeutic strategies, including androgenic modulation, to mitigate the elevated rejection risk associated with sex mismatch in corneal transplantation.

physiology↗

bioRxiv2025

Friend or foe: A mosquito parasite with mixed transmission mode displays mutualistic traits promoting oogenesis.

Mutualism is often selected in vertically transmitted symbionts due to their fitness interdependence with hosts. However, the evolution of mutualism remains unclear in symbionts using both vertical and horizontal transmission. In this study, we show that Ascogregarina taiwanensis, previously known as a weak horizontally transmitted parasite of the Asian tiger mosquito (Aedes albopictus), exhibits mutualistic traits that enhance mosquito reproduction. The symbiont improves embryogenesis and extends the egg-laying period while most females are pseudo-vertically transmitting symbiont oocysts to their progeny at oviposition sites. Dual transcriptomic analyses reveal that early oogenesis in infected females involves increased nitrogen metabolism in both partners, enhanced detoxification of blood waste, and activation of egg development pathways. These changes lead to improved assimilation of blood proteins essential for egg production. Our findings provide rare empirical evidence of a symbiont displaying both parasitic and mutualistic traits, offering new insights into the evolutionary dynamics of mixed-mode transmission symbioses. Significance StatementHow mutualism evolves from parasitism remains a central question in evolutionary biology, particularly for symbionts that combine vertical and horizontal transmission. We show that Ascogregarina taiwanensis, an Apicomplexan parasite previously known to be costly for developing Aedes albopictus mosquitoes, is also pseudo-vertically transmitted: most females release oocysts into the water during oviposition, exposing their offspring. Surprisingly, infection enhances host reproduction by promoting oogenesis through protein assimilation, leading to the production of larger larvae. Dual transcriptomic analyses reveal coordinated shifts in host and parasite metabolism, especially in nitrogen assimilation. Our findings provide rare evidence that mutualistic traits can emerge in a symbiont with mixed-mode transmission, offering new insights into the evolutionary transitions shaping host-microbe interactions.

evolutionary biology↗

bioRxiv2025

Differential conformational expansion of Nup98-HOXA9 oncoprotein in micro- and macrophases

Transcription factors (TFs) play a central role in gene regulation by binding to specific DNA sequences and orchestrating the transcriptional machinery. A majority of eukaryotic TFs have a block copolymer architecture, with at least one block being a folded DNA interaction domain, and another block being highly enriched in intrinsic disorder. Multivalent interactions in the intrinsically disordered region (IDR) can contribute to phase separation into macroscopic condensates. In this study, we focus on Nup98-HOXA9 (NHA9), a chimeric transcription factor implicated in leukemogenesis, in which two FG-repeat-rich IDRs derived from Nup98 get fused to the C-terminal part of transcription factor HOXA9. By integrating experiments and simulations, we examined the structural dynamics of NHA9s FG domain across assembly states. We found that the FG domain has different conformational compactness in the monomeric state, oligomeric, and densely packed condensate state. Notably, the oligomeric state exhibits micelle-like organisation, with the DNA-binding domain exposed at the periphery. While their architecture is non-random, their sizes depend on NHA9 concentration, consistent with non-core-shell spherical micelles. Molecular dynamics simulations support the expansion behaviour of NHA9s FG domain as oligomeric assemblies grow in size and reveal micelle-like structural features in oligomeric assemblies. These findings offer molecular insight into the phase behaviour of NHA9 and highlight the dynamic conformational transitions of IDRs during condensate formation, with implications for understanding transcriptional regulation in cancer.

biophysics↗

bioRxiv2025

Mechanistic Variability in Corneal Nerve Recovery Linked to Injury Type

The cornea, a transparent tissue covering the eye, is essential for clear vision and represents the most densely innervated tissue in the body. Its extensive sensory innervation provides both sensory perception and crucial trophic support, maintaining corneal health and integrity. Disruption of corneal innervation leads to neurotrophic keratitis (NK), a pathological condition caused by ocular injury, surgical procedures, or underlying diseases. The limited understanding of NKs pathophysiological mechanisms has hindered the development of innovative therapeutic approaches. In this study, we comparatively analyzed corneal innervation morphogenesis and regeneration across two clinically relevant injury models, highlighting both commonalities and differences among these contexts. Our results demonstrate that corneal nerve morphogenesis and maturation span approximately 13 weeks, from embryonic day 12 (E12) through three months of age. Additionally, we observed that the specification of distinct nerve fiber types coincided temporally with a significant enhancement in corneal sensitivity. Furthermore, we found that the type of innervation loss--either via axotomy or abrasion--differentially affected corneal sensitivity and epithelial cell homeostasis. Importantly, the regeneration mechanisms following injury were also distinctly dependent on the type of nerve damage sustained. Collectively, these findings underscore both the shared characteristics and unique aspects inherent in each NK model, highlighting the necessity for tailored therapeutic strategies specific to individual patterns of corneal innervation disruption.

neuroscience↗

bioRxiv2024

STING agonists drive recruitment and intrinsic type I interferon responses in monocytic lineage cells for optimal anti-tumor immunity

The cyclic GMP-AMP synthase-stimulator of interferon genes (cGAS-STING) pathway, a sensor of cytosolic DNA, orchestrates the production of pro-inflammatory cytokines, chemokines, and type I interferons (IFN-I), thereby contributing to spontaneous tumor surveillance. Intratumoral delivery of synthetic STING agonists induces IFN-I dependent tumor regression in preclinical cancer models and is being tested clinically. In this study, we investigate the role of monocytic lineage (MCs) cells in response to STING agonist induced IFN-I signaling. We show that CCR2-deficient mice, lacking inflammatory MCs in the periphery, or Lyz2-Cre-IFNAR1fl/fl mice in which IFN-I signaling in monocytes is reduced, exhibit impaired responses to STING agonist therapy of MC38 and/or B16F10 tumors. STING agonist treatment induced CCR5-dependent migration of MCs carrying tumor antigen from the tumor to the lymph nodes. Single-cell RNA sequencing of CD45+ cells from lymph nodes and tumors of mice in which half the hematopoietic cells lack the interferon alpha/beta receptor 1 (IFNAR1) revealed that STING agonist therapy induces intrinsic IFNAR1-dependent acquisition of an inflammatory monocytic cell phenotype distinct from inflammatory cDC and a reduction in macrophages with a pro-tumor TGF{beta}/angiogenesis transcriptome. IL-18 - IL-18R1 interaction was the top predicted interaction between monocytic lineage cells and CD8+T cells or NK cells. Blocking IL-18 reduced IFN-{gamma} production by CD8 T cells in LNs and decreased the therapeutic efficacy of STING agonist treatment in CCR2+/+ but not in CCR2-/- mice. These findings support a pivotal role for IL-18 producing inflammatory monocytic lineage cells in CD8 T cell control of melanoma following STING agonist treatment.

immunology↗

bioRxiv2024

Disordered proteins: microphases or associative polymers?

We develop a surrogate model for low complexity disordered proteins, which allows us to generate sequences with quantifiable disorder. We investigate properties of these sequences, and show that the sequence dependence of the radius of gyration only arises in the vicinity of the polymer collapse transition. Microphase propensity of the sequence is shown to be a reliable predictor, outperforming state of the art methods, in the crossover region. We show that predictions of associative polymer theory arises only as a limiting case, and discuss its applicability.

biophysics↗

bioRxiv2024

Inherited mitochondrial dysfunction triggered by OPA1 mutation impacts the sensory innervation fibre identity, functionality and regenerative potential in the cornea

Mitochondrial dysfunctions are detrimental to organ metabolism. The cornea, transparent outmost layer of the eye, is prone to environmental aggressions, such as UV light, and therefore dependent on adequate mitochondrial function. While several reports have linked corneal defects to mitochondrial dysfunction, the impact of OPA1 mutation, known to induce such dysfunction, has never been studied in this context. We used the mouse line carrying OPA1delTTAG mutation to investigate its impact on corneal biology. To our surprise, neither the tear film composition nor the corneal epithelial transcriptomic signature were altered upon OPA1 mutation. However, when analyzing the corneal innervation, we discovered an undersensitivity of the cornea upon the mutation, but an increased innervation volume at 3 months. Furthermore, the fibre identity changed with a decrease of the SP+ axons. Finally, we demonstrated that the innervation regeneration was less efficient and less functional in OPA1+/- corneas. Altogether, our study describes the resilience of the corneal epithelial biology, reflecting the mitohormesis induced by the OPA1 mutation, and the adaptation of the corneal innervation to maintain its functionality despite its morphogenesis defects. These findings will participate to a better understanding of the mitochondrial dysfunction on peripheral innervation.

pathology↗

bioRxiv2023

Effect of eye globe and optic nerve morphologies on gaze-induced optic nerve head deformations

PurposeTo investigate the effect of globe and optic nerve (ON) morphologies and tissue stiffnesses on gaze-induced optic nerve head deformations using parametric finite element modeling and a Design of Experiment (DOE) approach. MethodsA custom software was developed to generate finite element models of the eye using 10 morphological parameters: dural radius, scleral, choroidal, retinal, pial, peripapillary border tissue thicknesses, prelaminar tissue depth, lamina cribrosa (LC) depth, ON radius, and ON tortuosity. A 10-factor 2-level full-factorial analysis (1,024 models) was used to predict the effects of each morphological factor and their interactions on LC strains induced by 13{degrees} adduction. Subsequently, a further DOE analysis (1,024 models) was conducted to study the effects and potential interactions between the top 5 morphological parameters identified from the initial DOE study and 5 critical tissue stiffnesses. ResultsIn the DOE analysis of 10 morphological parameters, the five most significant factors were ON tortuosity, dural radius, ON radius, scleral thickness and LC depth. Further DOE analysis incorporating biomechanical parameters highlighted the importance of dural and LC stiffness. A larger dural radius and stiffer dura increased LC strains but the other main factors had the opposite effects. Notably, a significant interaction was found between dural radius and dural stiffness. ConclusionsThis study highlights the significant impact of morphological factors on LC deformations during eye movements, with key morphological effects being more pronounced than tissue stiffnesses.

bioengineering↗

bioRxiv2023

Gaining Biological Insights through Supervised Data Visualization

Dimensionality reduction-based data visualization is pivotal in comprehending complex biological data. The most common methods, such as PHATE, t-SNE, and UMAP, are unsupervised and therefore reflect the dominant structure in the data, which may be independent of expert-provided labels. Here we introduce a supervised data visualization method called RF-PHATE, which integrates expert knowledge for further exploration of the data. RF-PHATE leverages random forests to capture intricate featurelabel relationships. Extracting information from the forest, RF-PHATE generates low-dimensional visualizations that highlight relevant data relationships while disregarding extraneous features. This approach scales to large datasets and applies to classification and regression. We illustrate RF-PHATEs prowess through three case studies. In a multiple sclerosis study using longitudinal clinical and imaging data, RF-PHATE unveils a sub-group of patients with non-benign relapsingremitting Multiple Sclerosis, demonstrating its aptitude for time-series data. In the context of Raman spectral data, RF-PHATE effectively showcases the impact of antioxidants on diesel exhaust-exposed lung cells, highlighting its proficiency in noisy environments. Furthermore, RF-PHATE aligns established geometric structures with COVID-19 patient outcomes, enriching interpretability in a hierarchical manner. RF-PHATE bridges expert insights and visualizations, promising knowledge generation. Its adaptability, scalability, and noise tolerance underscore its potential for widespread adoption.

bioinformatics↗

bioRxiv2023

REGENERATIVE GENE THERAPY IN THE HYPOTHALAMUS PROLONGS FERTILITY IN FEMALE RATS

There is substantial evidence that age-related ovarian failure in rats is preceded by abnormal responsiveness of the neuroendocrine axis to estrogen positive feedback. In middle-aged (M-A) female rats, we have demonstrated that intrahypothalamic gene therapy for insulin-like growth factor-I (IGF-I) started at 6 months of age extends the regular cyclicity of the animals beyond 10 month (the age at which MA rats stop ovulating) and preserves the integrity of the ovarian structure. Here, we implemented long-term regenerative gene therapy in the hypothalamus of young females. The goal was to extend fertility in the treated animals. We constructed a helper-dependent adenovector that harbors the green fluorescent protein (GFP) reporter gene as well as a gene tandem, termed STEMCCA, which harbors the 4 Yamanaka genes (oct4, sox2, klf4, and c-myc, OSKM), both under the control of a Tet-Off bidirectional promoter. An adenovector that only carries the gene for GFP was used as control. At 4 months of age 12 female rats received an intrahypothalamic injection of our OSKM-GFP vector (treated rats); 12 control rats a vector expressing GFP only (control rats). At 9.3 months of age control and treated rats were mated with young males. A group of 12 young intact female rats was also mated. The rate of pregnancy recorded was 83%, 8.3% and 25% for young, M-A control and M-A treated animals, respectively. Average litter size was 9, 3 and 3 for the corresponding groups. Mean pup BW was slightly higher in the M-A rats. In a preliminary study we confirmed that ovulation in our M-A females ceases at 10 months of age. Our results are in line with the evidence that viral vector-mediated delivery of the Yamanaka genes in the brain has strong regenerative effects without adverse side effects. The particular significance of the present results is that, for the first time, they show that long-term OSKM gene therapy in the hypothalamus is able to extend the functionality of such a complex system as the hypothalamo-pituitary-ovarian axis.

neuroscience↗

bioRxiv2023

Estimating the energy requirements for long term memory formation

Brains consume metabolic energy to process information, but also to store memories. The energy required for memory formation can be substantial, for instance in fruit flies memory formation leads to a shorter lifespan upon subsequent starvation (Mery and Kawecki, 2005). Here we estimate that the energy required corresponds to about 10mJ/bit and compare this to biophysical estimates as well as energy requirements in computer hardware. We conclude that while the reason behind it is not known, biological memory storage is metabolically expensive,

neuroscience↗

bioRxiv2020

Heterochromatin flexibility contributes to chromosome segregation in cell nucleus

While there is a prevalent genome organization in eukaryotic cells, with heterochromatin concentrated at the nuclear periphery, anomalous cases do occur. Deviations of chromatin distribution are frequent, for example, upon aging, under malignant diseases, or even naturally in rod cells of nocturnal mammals. Using molecular dynamic simulations, we study the segregation of heterochromatin in the cell nucleus by modeling interphase chromosomes as diblock ring copolymers confined in a rigid spherical shell. In our model, heterochromatin and euchromatin are distinguished by their bending stiffnesses, while an interaction potential between the spherical shell and chromatin is used as a proxy for lamin-associated proteins. Our simulations indicate that in the absence of attractive interactions between the nuclear shell and the chromatin, the majority of heterochromatin segregates towards the nuclear interior due to depletion of less flexible heterochromatin segments from the nuclear periphery. This inverted chromatin distribution is in accord with experimental observations in rod cells. This "inversion" is also found to be independent of the heterochromatin concentration and chromosome number, and is further enhanced by additional attractive interactions between heterochromatin segments. as well as by allowing bond-crossing to emulate topoisomerase activity. The usual chromatin distribution, with heterochromatin at the periphery, can be recovered by further increasing the bending stiffness of heterochromatin segments or by turning on attractive interactions between the nuclear shell and heterochromatin. Overall, our results indicate that bending stiffness of chromatin could be a contributor to chromosome organization along with differential effects of HP1-driven phase segregation and of loop extruders, and interactions with the nuclear envelope and topological constraints.

biophysics↗