Biology subjects

Chen, L.

Publications and source records attributed to Chen, L..

At least 307 records · Page 17Linked to original sources

bioRxiv2025

Somatic mutations distinguish melanocyte subpopulations in human skin

To better understand the homeostatic mechanisms governing melanocytes, we performed deep phenotyping of clonal expansions of single melanocytes from human skin. In total, we interrogated the mutational landscapes, gene expression profiles, and morphological features of 297 melanocytes from 31 donors. To our surprise, a population of melanocytes with low mutation burden was maintained in sun damaged skin. These melanocytes were more stem-like, smaller, less dendritic and displayed distinct gene expression profiles compared to their counterparts with high mutation burdens. We used single-cell spatial transcriptomics (10X Xenium) to reveal the spatial distribution of melanocytes inferred to have low and high mutation burdens (LowMut and HighMut cells), based on their gene expression profiles. LowMut melanocytes were found in hair follicles as well as in the interfollicular epidermis, whereas HighMut melanocytes resided almost exclusively in the interfollicular epidermis. We propose that melanocytes in the hair follicle occupy a privileged niche, protected from UV radiation, but periodically migrate out of the hair follicle to replenish the interfollicular epidermis after waves of photodamage. More broadly, our study illustrates the advantages of a cell atlas that includes mutational information, as cells can change their cellular states and positional coordinates over time, but mutations are like scars, providing a historical record of the homeostatic processes that were operative on each cell.

cell biology↗

bioRxiv2025

Single-Cell Transcriptomics Reveals Dynamic Microglial States and Neural-Immune Networks in Human Diabetic Retinopathy

Diabetic retinopathy (DR) is a major cause of vision loss worldwide. Here, we conduct single-cell RNA sequencing of twenty human retina samples (from living and post-mortem donors) across non-diabetic, diabetic, and DR states to create a comprehensive transcriptomic atlas. We identify two stable microglial populations--homeostatic and inflammatory--that exist along a functional continuum, plus a neutrophil cluster within C1QA+ myeloid cells with dynamic transitions occurring throughout disease progression. Module-level analysis reveals divergent transcriptional trajectories: homeostatic microglia maintain energetic programs while selectively upregulating stress elements, whereas inflammatory microglia layer additional pro-inflammatory programs onto preserved biosynthetic foundations. Eleven co-expression modules organize into two major axes: an inflammatory-stress axis, and a regulatory/metabolic-motility axis, with a stable translation module persisting across disease stages. Cell communication analysis further highlights sophisticated neural-immune interactions, particularly between photoreceptors and microglia. Our findings provide insights into the complex cellular dynamics of DR progression and suggest potential therapeutic targets for early intervention.

bioinformatics↗

bioRxiv2025

Estimation of total mediation effect for a binary trait in a case-control study for high-dimensional omics mediators

Mediation analysis helps uncover how exposures impact outcomes through intermediate variables. Traditional mean-based total mediation effect measures may suffer from the cancellation of opposite component-wise effects, and existing methods often lack the power to capture weak effects in high-dimensional mediators. Additionally, most high-dimensional mediation analysis methods have focused on continuous outcomes, with limited attention to binary outcomes, particularly in case-control studies. To fill this gap, we propose an R2 total mediation effect measure within the liability framework that offers a clear and intuitive causal interpretation, provides additional insights beyond the mean-based measures, and is invariant to disease prevalence. We develop a cross-fitted, modified Haseman-Elston regression-based estimation procedure tailored for mediation analysis in case-control studies, which can also be applied to cohort studies. Our estimator remains consistent in the presence of non-mediators and weak effects, as demonstrated in extensive simulations. Theoretical justification for consistency is provided under mild conditions and without requiring exact mediator selection. In a case-control substudy of the Womens Health Initiative involving 2150 individuals, we found that many metabolites were mediators with weak effects in the path from BMI to coronary heart disease, and we estimated that 89% (95% CI: 57%-100%) of the BMI-explained variation in underlying CHD liability is mediated by the measured metabolomics. The proposed estimation procedure is implemented in the R package "r2MedCausal", available on GitHub.

genomics↗

bioRxiv2025

Fluorescence Lifetime Imaging Microscopy (FLIM) visualizes internalization and biological impact of nanoplastics in live intestinal organoids

The increasing micro- and nanoplastic (MNP) pollution poses significant risks to human and animal health, yet the mechanisms of their accumulation and effects on absorptive tissues such as the gastrointestinal tract remain poorly understood. Addressing these knowledge gaps requires tractable models coupled to dynamic live cell imaging methods, to enable multi-parameter analysis at single cell resolution. Here we report a new method combining adult stem cell-derived small intestinal organoid cultures with multi-parameter live Fluorescence Lifetime Imaging Microscopy (FLIM) to study MNP interactions with gut epithelium. To facilitate this, we optimized live imaging of porcine and mouse small intestinal organoids with an apical-out topology. Subsequently, we produced a set of pristine MNPs based on PMMA and PS (<200 nm, doped with deep-red fluorescent dye) exhibiting different surface charges, and evaluated their interaction with organoids displaying controlled epithelial polarity. We found that nanoparticles differently interacted with apical and basal membranes of the organoids and even showed a species-specific pattern of cellular uptake. Using a phasor-FLIM approach, we demonstrate better sensitivity of FLIM over conventional intensity-based microscopy. The fluorescence lifetime barcoding enabled distinguishing different types of MNP and their interaction sites within organoids. Finally, we studied short (1 day)- and long (3 days)-term exposure effects of PMMA and PS-based MNPs on mitochondrial function, total energy budget and epithelial inflammation and found that even pristine MNPs could disrupt chemokine production and mitochondrial membrane potential in intestinal epithelial cells. The presented FLIM approach will advance the study of MNP toxicity, their biological impacts on gastrointestinal tissue and help tracing other types of fluorescent nanoparticles in live organoid and 3D ex vivo systems.

pharmacology and toxicology↗

bioRxiv2025

The expression of IL-35 in the prophase of liver failure and its preliminary exploration for the mechanism of immunoregulation by IL-35 and glucocorticoids

Background and AimsTo determine appropriate dosages for mice models in liver failure prophase and explore IL-35 and cytokine levels. Also, investigate changes in Treg/ Th17 ratio, IL-35, and IL-17 in patients with HBV-induced liver failure before and after treatment. MethodsWe induced liver failure in mice with different doses of concanavalin and assessed severity through serum biochemistry and pathology. Mice were divided into control, model, IL-35 plasmid, anti-IL-35, and dexamethasone groups. IL-35 and IL-17 expressions in liver tissue were evaluated via immunohistochemistry, fluorescence staining, and ELISA. Treg/Th17 ratio and IL-35 and IL-17 levels in peripheral blood of patients were measured using flow cytometry and ELISA, compared to 22 healthy individuals. ResultsThe optimal dose for the liver failure model was 20 g/ kg concanavalin. The IL-35 plasmid and dexamethasone groups showed significantly lower serum TBil, ALT, AST, IL-4, IL-17, TNF- , and liver histopathology scores compared to the model group, while the anti-IL-35 group showed higher levels (P<0. 05). In HBV-PLF patients, TBil, ALT, and AST significantly decreased, and PTA increased after glucocorticoid treatment (P<0. 05). Treg/ Th17 ratio was lower in HBV-PLF patients compared to the healthy group (P<0. 05), with higher IL-35 and IL-17 levels (P<0. 05). Post-treatment, Treg increased and Th17 decreased significantly; IL-17 and Treg/ Th17 ratios increased, while IL-35 decreased (P<0.05). IL-35 positively correlated with the Treg/Th17 ratio. Conclusions 20 g/ kg concanavalin proper dose for mice model. IL-35 may protect in liver failure. Glucocorticoids help maintain immune balance, prevent failure, increase ratios and IL-35 in HBV-PLF patients, and IL-35 related to Treg/Th17 balance.

immunology↗

bioRxiv2025

The biochemical function of bivalent aptamer assemblies against B-cell markers CD19 and CD20

Aptamers are synthetic oligonucleotides that bind to their specific receptors with high specificity, offering immense potential for the development of molecular tools. Using recently introduced Ligand-Guided Selection (LIGS), a variant of the Systematic Evolution of Ligands by Exponential Enrichment (SELEX) we previously identified anti-CD19 and anti-CD20 aptamers with specificity and affinity. Given their high expression levels, B-cell markers CD19 and CD20 are widely utilized in the diagnosis of B-cell-related malignancies and autoimmune diseases. Here, we report the design and functional characterization of bivalent aptamer assemblies targeting CD19 and CD20 expressed in B-cell lymphomas. Using a strategic approach, we synthesized dimeric constructs of these aptamers with polyethylene glycol (PEG) linkers of varying lengths to tether the two aptamer units. The bivalent aptamers demonstrated enhanced binding affinity and specificity, with an optimal linker length of [~]3.96 nm. Functional studies revealed that dimeric CD19 aptamers selectively internalized in CD21-negative B-cells, while CD20 aptamers exhibited improved antigen binding without triggering calcium release. These findings highlight the potential of bivalent aptamers in engineering cost-effective, stable, and precise therapeutic agents for B-cell-related malignancies, such as diffuse large B-cell lymphoma (DLBCL). This work advances the development of aptamer-based synthetic therapeutics with promising clinical applications.

biochemistry↗

bioRxiv2025

Concurrent PIK3CA mutant drives cachexia through inflammatory signaling in EGFR mutant lung cancer

PIK3CA mutation is frequently concurrent with known oncogenic drivers such as EGFR mutation in lung cancer, raising an interesting question about its real function. Cachexia is a systemic disease involving complex interaction between primary tumors and distant organs, significantly contributing to cancer-related mortality. Through integrative study of genetically engineered mouse models (GEMMs) and clinical data, we find concurrent PIK3CA mutant preferentially drives cachexia in EGFR-mutant lung cancer, promoting malignant progression instead of cancer initiation. PIK3CA mutant-mediated cachexia could be overcome by osimertinib (Osi) treatment in Osi-sensitive GEMM. In contrast, chemotherapy, routinely used in clinic for those relapsed from Osi therapy, fails to ameliorate cachexia in Osi-resistant GEMM despite notable tumor suppression. PIK3CA mutant-driven cachexia is mediated through NF-{kappa}B activation and could be dampened by combined aspirin treatment. This work uncovers the biological function of PIK3CA mutant and mechanism behinds its clinical impacts, and proposes a potentially effective strategy for clinical management.

cancer biology↗

bioRxiv2025

Sequencing-based Spatial Transcriptomics with scRNA-seq Sensitivity

The advent of spatial transcriptomics has dramatically expanded our ability to study the vast network of cell-cell interactions at the molecular level in tissue. Among current methods, sequencing-based approaches have great potential in discovering because of its unbiased capture. In the last couple of years, the spatial resolution for the capture addresses has been significantly improved from 100 m to <1 m, well below the size of a mammalian cell. However, the capture efficiency has always been a pain point, [~]one order of magnitude lower than that of single cell RNA sequencing (scRNA-seq). The low capture efficiency limits the depth and breadth of its applications in the study of complex biological systems and diseases. Here, we introduce Salus Spatial transcriptomic system (Salus-STS), which provides [~]1 m capture resolution and a capture efficiency [~]1 order of magnitude higher than other current methods. Analysis with sub-cellular resolution becomes practical for sequencing-based spatial transcriptomics.

molecular biology↗

bioRxiv2025

VZV gE Promotes STING Degradation via Midnolin-Proteasome Pathway to Inhibit cGAS-STING Signaling

Varicella-zoster virus (VZV) infects 85 million individuals annually and it is known for its intricate interplay with host cellular mechanisms, significantly impacting antiviral immune responses. Previous studies have highlighted the critical role of VZV glycoprotein E (gE) in virus-host interactions, but the precise mechanisms remain to be elucidated. Our results demonstrate that VZV gE interacts with STING, specifically through the gE (350-480aa) and STING (151-160aa) regions. This interaction predominantly involves incompletely glycosylated gE. Functional assays revealed that gE inhibits the cGAS-STING signaling pathway. gE enhances VZV proliferation and promotes STING degradation via the proteasome pathway, without affecting STING ubiquitination. We identified Midnolin as a mediator in this degradation process, with gE facilitating the interaction between STING and Midnolin. In vivo, gE expression in mice led to diminished antiviral responses upon HSV-1 infection, highlighting gEs role in modulating immune signaling. Our findings provide significant insights into VZVs evasion of host immune responses. By promoting STING degradation through an unconventional Midnolin-proteasome pathway, VZV gE effectively suppresses antiviral signaling, facilitating enhanced viral proliferation. The findings contribute significantly to the understanding of VZV pathogenesis and provide new therapeutic strategies against VZV.

microbiology↗

bioRxiv2025

AUTO-SP: automated sample preparation for analyzing proteins and protein modifications

Liquid chromatography (LC) tandem mass spectrometry (MS/MS) is one of the widely used proteomic techniques to study the alterations occurred at protein expression level as well as post-translation modifications (PTMs) of proteins that are relevant to different physiological or pathological statuses. The mass spectrometric analysis of peptides fragmented from proteins (bottom-up proteomics) has emerged as one of the major approaches for proteomics. In this approach, proteins are first cleaved into peptides for mass spectrometric analysis and peptides with PTMs are further enriched followed by the LC-MS/MS analysis. To achieve a reproducible and quantitative proteomic characterization, a well-established protease digestion and PTM peptide enrichment protocol is critical. In this study, we developed an automated sample preparation (AUTO-SP) for analyzing proteins and protein modifications utilizing Patient-Derived Xenograft (PDX) breast cancer tumors (basal-like and luminal subtypes). The protein amount was quantified and proteins were further digested by using AUTO-SP for each PDX sample. Based on the data-independent acquisition (DIA)-MS data, we observed samples of the same breast cancer subtypes were highly correlated (>0.98). Additionally, >14,000 ubiquitinated peptides were identified in the PDX samples when using AUTO-SP for ubiquitin enrichment, while unique pathways were enriched from the basal-like and luminal subtypes. AUTO-SP demonstrated its efficacy to provide reliable and reproducible sample preparation procedure for MS-based proteomic and PTM analyses.

systems biology↗

bioRxiv2025

Food pairing independently associated with cardiometabolic traits beyond dietary patterns across western and eastern populations

Cardiometabolic health is closely linked to diet. Both specific food choices and dietary indices are commonly used to guide cardiometabolic protection strategies. However, the balance between foods may also significantly impact cardiometabolic health. Here, we explore the balance and imbalance in long-term dietary food intake to quantify food pairing patterns (FPs), providing insights beyond conventional dietary indices and single-food intake frequencies. Using data from our GGMP (n = 6,994) and the NHANES (n = 7,350) cohorts, we observed that long-term food pairing patterns are independent of single food intake frequency and dietary indices. We identified 1,759 and 306 cardiometabolic-related long-term food pairing patterns from two cohorts (FDR < 0.05), respectively. Notably, around 80% of these pairing foods not individually associated with cardiometabolic traits, and food pairing pattern associations with cardiometabolic traits at hyper food group level were consistent across Eastern and Western populations. Besides, mediation analysis revealed that 72.7% of long-term food pairing patterns affected cardiometabolic traits through 31 microbial genera, with Clostridiumsensustricto1 playing a predominant role. Moreover, multi-step mediation analysis found that microbes mediated the impact of long-term food pairing patterns on cardiometabolic traits primarily through their metabolic pathways, such as pyruvate fermentation to propanoate and ergothioneine biosynthesis pathways. Our data suggest that balance between dietary foods is broadly associated with cardiometabolic traits by modulating gut microbial functionalities, in contrast to the lower occurrence when considering individual foods in isolation. These results offer a novel perspective for designing personalized dietary strategies beyond present dietary indices to enhance cardiometabolic health.

microbiology↗

bioRxiv2024

The genetic diversity and populational specificity of the human gut virome at single nucleotide resolution

Large-scale characterization of gut viral genomes provides strain-resolved insights into host-microbe interactions. However, existing viral genomes are mainly derived from Western populations, limiting our understanding of global gut viral diversity and functional variations necessary for personalized medicine and addressing regional health disparities. Here, we introduce the Chinese Gut Viral Reference (CGVR) set, consisting of 120,568 viral genomes from 3,234 deeply sequenced fecal samples collected nationwide, covering 72,751 viral species-level clusters (VSCs), nearly 90% of which are absent from current databases. Analysis of single nucleotide variations (SNVs) in 233 globally prevalent VSCs revealed that 18.9% showed significant genetic stratification between Chinese and non-Chinese populations, potentially linked to bacterial infection susceptibility. The predicted bacterial hosts of population-stratified viruses exhibit distinct genetic components associated with health-related functions, including multidrug resistance. Additionally, viral strain diversity at the SNV level correlated with human phenotypic traits, such as age and gastrointestinal issues like constipation. Our analysis also indicates that the human gut bacteriome is specifically shaped by the virome, which mediates associations with human phenotypic traits. This foundational resource underscores the unique genetic makeup of the gut virome across populations and emphasizes the importance of recognizing gut viral genetic heterogeneity for deeper insights into regional health implications.

microbiology↗

bioRxiv2024

Spatial heterogeneity influences phage-host co-existence dynamics and phage resistance development in Vibrio anguillarum

Exposure of bacterial populations to phage infection pressure is a significant driver of phage-host co-evolution and diversification. However, the impact of the spatial organization of bacterial population co-existence and co-evolution dynamics remains poorly understood. Here, we investigated how the spatial structure of the host population affects phage-host interactions by co-cultivating a Vibrio anguillarum strain with the lytic T4-like vibriophage KVP40 under conditions that resulted in either a homogenous, well-mixed population or a heterogeneous population with bacterial aggregates. We observed markedly different temporal dynamics associated with the two population structures over a 30-day adaptive laboratory evolution experiment. Phage and host dynamics suggested that phage-sensitive subpopulations retained in the aggregates substantially prolonged the coexistence of phages and bacteria, relative to the homogenous environment. However, the limited phage propagation on the sensitive subpopulations was insufficient for host range expansion to occur. In contrast, daily supplementation of sensitive host bacteria in parallel experiments readily led to the emergence of phage mutants with enhanced infective capability and an expanded host range. These results underscore the importance of bacterial spatial organization in determining the outcome of phage attacks and highlight the complex interplay between genomic processes and ecological conditions in driving evolutionary innovations.

microbiology↗

bioRxiv2024

Sub-second characterization of locomotor activities of mouse models of Parkinsonism

The degeneration of midbrain dopamine (DA) neurons disrupts the neural control of natural behavior, such as walking, posture, and gait in Parkinsons disease. While some aspects of motor symptoms can be managed by dopamine replacement therapies, others respond poorly. Recent advancements in machine learning-based technologies offer opportunities to better understand the organizing principles of behavior modules at fine time scales and its dependence on dopaminergic modulation. In the present study, we applied the motion sequencing (MoSeq) platform to study the spontaneous locomotor activities of neurotoxin and genetic mouse models of Parkinsonism as the midbrain DA neurons progressively degenerate. We also evaluated the treatment efficacy of levodopa (L-DOPA) on behavioral modules at fine time scales. We revealed robust changes in the kinematics and usage of the behavioral modules that encode spontaneous locomotor activity. Further analysis demonstrates that fast behavioral modules with higher velocities were more vulnerable to loss of DA and preferentially affected at early stages of Parkinsonism. Last, L-DOPA effectively improved the velocity, but not the usage and transition probability, of behavioral modules in Parkinsonian animals. In conclusion, the hypokinetic phenotypes in Parkinsonism involve the decreased velocities of behavioral modules and their disrupted temporal organization during movement. Moreover, we showed that the therapeutic effect of L-DOPA is mainly mediated by its effect on the velocities of behavior modules at fine time scales. This work documents robust changes in the velocity, usage, and temporal organization of behavioral modules and their responsiveness to dopaminergic treatment under the Parkinsonian state. Significance StatementParkinsons disease is the second largest neurodegenerative disease without a cure. Detection of subtle Parkinsonian signs is critical for disease-modification by applying early interventions. The present work explores the possibility of using machine learning-based approaches for early detection of subtle behavioral changes in Parkinsonian animals and evaluating the therapeutic efficacy of dopaminergic medications.

neuroscience↗

bioRxiv2024

Engineering tissue-mimetic hydrogels with continuous viscoelastic gradient for programmed cell migration

The dynamic, viscoelastic nature of the extracellular matrix (ECM), with variations in stiffness and viscosity, plays a key role in cellular behaviors like mechano-sensing, migration, and force generation. Viscoelastic hydrogels are important for mimicking the ECM to study cell migration and tissue engineering. However, creating hydrogels with continuous viscoelastic gradients is challenging due to issues with spatial resolution, reproducibility, and accurately replicating native tissue properties. Here we present a novel approach to generate hydrogels with precisely controllable viscoelastic gradients using drop-by-drop condensation. This approach allows fine-tuned replication of the tissue-specific local mechanical properties, resulting in hydrogels of heterogeneous viscoelasticity. Directed migration and separation of multiple cell lines are thus driven by local viscosity and elasticity rather than solely stiffness. By incorporating non-linear mechanical gradients, this technique provides insights into ECM viscoelasticitys role in cellular behavior and offers a versatile platform for advanced tissue engineering and regenerative medicine applications.

biophysics↗

bioRxiv2024

Development of a novel peripherally acting alpha2A-adrenergic receptor antagonist for anti-diabetic

Yohimbine, a potent alpha2A-adrenergic receptor (2AAR) antagonist, was found therapeutic potential for type 2 diabetes through improving insulin release. However, the adverse side effects mediated by its actions in the brain hampered its use. Here, based on molecular docking analysis and structural modification, we have developed a novel peripherally acting yohimbine derivative (CDS479-2). CryoEM data found that yohimbine and CDS479-2 have similar interactions with the structure of 2AAR. Importantly, CDS479-2 shows similar 2AAR antagonist activity as yohimbine, but with very limited access to the brain, and thus avoiding the unwanted central effects such as hypertension and anxiety. Acute administration of CDS479-2 by injection or gavage lowered blood glucose levels and improved glucose tolerance in the high-fat diet-induced obesity (DIO) mice, an animal model for human type 2 diabetes. Remarkably, DIO mice received 2 weeks of daily administration of CDS479-2, but not yohimbine, exhibited sustained normoglycaemia, and increased density of the insulin-producing beta cells, in which important proliferation genes were found upregulated. Moreover, the overall protein expression levels of their pancreas were more similar to that of the healthy chow-fed mice. Thus, CDS479-2 may indicate a new direction for type 2 diabetes treatment. Importantly, the strategy we employed in this study will inspire the optimization for drugs that with both peripheral and central targets. Graphic abstract O_FIG O_LINKSMALLFIG WIDTH=166 HEIGHT=200 SRC="FIGDIR/small/628818v1_ufig1.gif" ALT="Figure 1"> View larger version (49K): org.highwire.dtl.DTLVardef@1d3d7corg.highwire.dtl.DTLVardef@1afbad3org.highwire.dtl.DTLVardef@12a1aborg.highwire.dtl.DTLVardef@1341a02_HPS_FORMAT_FIGEXP M_FIG C_FIG

pharmacology and toxicology↗

bioRxiv2024

Structural maturation of the matrix lattice is not required for HIV-1 particle infectivity

HIV-1 assembly is initiated by the binding of Gag polyproteins to the inner leaflet of the plasma membrane, mediated by the myristylated matrix (MA) domain of Gag. Subsequent to membrane binding, Gag oligomerizes and buds as an immature, non-infectious virus particle, which, upon cleavage of the Gag precursor by the viral protease, transforms into a mature, infectious virion. During maturation, the MA lattice underlying the viral membrane undergoes a structural rearrangement and the newly released capsid (CA) protein forms a mature capsid that encloses the viral genome. While it is well established that formation of the mature capsid is essential to particle infectivity, the functional role of MA structural maturation remains unclear. Here, we examine MA maturation of an MA triple mutant, L20K/E73K/A82T, which exhibits distinct biochemical behaviours. The L20K/E73K/A82T mutant is a revertant derived by propagating the L20K mutant, which exhibits reduced infectivity and increased association of the Gag polyprotein with membranes. L20K/E73K/A82T replicates similarly to wild type but retains the increased Gag membrane binding properties of L20K. L20K/E73K/A82T MA also sediments to high-density fractions in sucrose gradients after detergent treatment under conditions that fully solubilize WT MA, suggesting enhanced MA-MA interactions. Cryo-electron tomography with subtomogram averaging reveals that the immature MA lattice of L20K/E73K/A82T closely resembles the wild type. However, mature virions of the triple mutant lack a detectable MA lattice, in stark contrast to both the wild type and L20K mutant. All-atom molecular dynamics simulations suggest that this absence results from destabilized inter-trimer interactions in the mature L20K/E73K/A82T MA. Furthermore, introducing additional mutations designed to disrupt the mature MA lattice does not impair particle infectivity. These findings suggest that an ordered, membrane-associated mature MA lattice is not essential for HIV-1 infectivity, providing new insights into the structural plasticity of the matrix during maturation and its functional role in the viral lifecycle.

microbiology↗

bioRxiv2024

Nucleosome Spacing Can Fine-Tune Higher Order Chromatin Assembly

Cellular chromatin displays heterogeneous structure and dynamics, properties that control diverse nuclear processes. Models invoke phase separation of conformational ensembles of chromatin fibers as a mechanism regulating chromatin organization in vivo. Here we combine biochemistry and molecular dynamics simulations to examine, at single base-pair resolution, how nucleosome spacing controls chromatin phase separation. We show that as DNA linkers extend from 25 bp to 30 bp, as examplars of 10N+5 and 10N (integer N) bp lengths, chromatin condensates become less thermodynamically stable and nucleosome mobility increases. Simulations reveal that this is due to trade-offs between inter- and intramolecular nucleosome stacking, favored by rigid 10N+5 and 10N bp linkers, respectively. A remodeler can induce or inhibit phase separation by moving nucleosomes, changing the balance between intra- and intermolecular stacking. The intrinsic phase separation capacity of chromatin enables fine tuning of compaction and dynamics, likely contributing to heterogeneous chromatin organization in vivo.

biophysics↗