Biology subjects

Yuan, Y.

Publications and source records attributed to Yuan, Y..

At least 55 records · Page 3Linked to original sources

bioRxiv2026

ISPpu10 is a structure-gated bridge RNA recombinase that drives safe, large-scale genomic plasticity

IS110 elements employ bridge RNA to direct target site recognition, yet whether additional layers of specificity exist beyond RNA-DNA base pairing is unknown. Here we identified ISPpu10, an IS110 element in Pseudomonas putida that is associated with >100-kb segmental amplifications during adaptive laboratory evolution. All insertions mapped to multiple identical copies of a single conserved intergenic sequence harboring a GC-rich 5' extension that forms a stem-loop. Systematic mismatch and compensatory substitution scanning revealed a sequence-structure dual-match logic: base pairing between the bridge RNA and target DNA serves as an RNA-guided match, whereas the target-encoded stem-loop provides an additional specificity determinant. Transplanting this stem-loop into Escherichia coli targets improved on-target integration and reduced genome-wide off-target insertion, establishing the stem-loop as a portable structural gate. These findings reveal a structural recognition layer beyond base-pairing, suggesting how bacteria reconcile transposition with genome integrity and offering a strategy for precise genome editing.

microbiology↗

bioRxiv2026

UniST: A Unified Computational Framework for 3D Spatial Transcriptomics Reconstruction

Spatial transcriptomics (ST) enables the measurement of gene expression in its native spatial context, yet most ST datasets are acquired as two-dimensional (2D) sections. Consequently, the underlying three-dimensional (3D) organization of tissues is only partially observed, and 3D ST data generated from serial sections are typically sparse and heterogeneous, with substantial tissue loss and missing measurements. These limitations pose major analytical challenges for reconstructing coherent 3D tissue architecture, rather than issues of experimental scalability alone. Here, we present UniST, a unified generative artificial intelligence (AI) framework designed to computationally reconstruct dense and continuous 3D ST landscapes from sparse serial sections, without altering the underlying experimental ST technologies. UniST integrates three complementary modules: kernel point convolution with cross-attention layers for point cloud upsampling, optical flow-based interpolation for continuous slice reconstruction, and a graph autoencoder with implicit neural representations for gene expression imputation. Together, these components densify sparse slices, resolve discontinuities, and map spatial coordinates to high-dimensional transcriptomics. Across multiple ST platforms and tissue contexts, UniST accurately restored structural continuity and biologically meaningful expression patterns. In a mouse embryo dataset, UniST reconstructed a dense 3D heart architecture from sparsely sampled slices. In two 3D human cancer tissues, UniST recovered critical spatial features, including tumor-immune boundaries and tertiary lymphoid structures, that were fragmented in the original data. By providing a generalizable computational solution that complements existing ST acquisition protocols, UniST facilitates cost-efficient and scalable reconstruction of 3D ST landscapes, enabling more faithful investigation of tissue organization and disease biology.

bioinformatics↗

bioRxiv2026

PRMT5-Mediated Arginine Methylation of HSP90AA1 Drives Esophageal Squamous Cell Carcinoma Progression

Dysregulated HSP90AA1 chaperone activity is a hallmark of multiple human cancers, yet its post-translational modifications in esophageal squamous cell carcinoma (ESCC) are poorly defined. Here, we identify a PRMT5-driven modification of HSP90AA1, symmetric dimethylation at arginine 182 (R182), as a pivotal switch that fuels ESCC progression. HSP90AA1 physically associates with PRMT5, and genetic or pharmacologic PRMT5 blockade diminishes HSP90AA1-R182 methylation and downstream oncogenic signaling. Functionally, HSP90AA1 loss suppresses ESCC cell proliferation, migration, and invasion; enforces cell cycle arrest and reverses epithelial-mesenchymal transition (EMT). Re-expression of wild-type HSP90AA1 rescues cancer cell growth and EMT in vitro and in vivo, whereas the methylation-deficient R182A mutant does not. Furthermore, clinically oriented analysis shows HSP90AA1 overexpression in ESCC tissues and indicates moderate prognostic utility. Moreover, dual targeting of the PRMT5/HSP90AA1 axis is therapeutically attractive, and combined PRMT5/HSP90AA1 inhibition acts synergistically to exert anti-tumor activity, markedly reducing clonogenicity, invasion, and tumor burden in both cell-derived and patient-derived xenograft models. These findings demonstrate that PRMT5/HSP90AA1 serve as mechanistic drivers and actionable biomarkers in ESCC and provide a rationale for biomarker-guided co-inhibition of PRMT5/HSP90AA1 in translational studies.

cancer biology↗

bioRxiv2026

Pharmacological recruitment of a VTA glutamatergic arousal circuit by the natural product BN3 drives broad-spectrum emergence from general anesthesia

Pharmacological control of emergence from general anesthesia remains strikingly limited. Clinically available antagonists are largely drug-class specific, leaving recovery dependent on anesthetic clearance rather than to an actively programmable switch in brain state. Through phenotypic screening of a structurally diverse natural-product library, we identified BN3 (L-(-)-camphor) as a broad-spectrum emergence agent. BN3 robustly shortened recovery from propofol anesthesia across species--from mice and rats to rabbits, dogs, and rhesus monkeys--and remained effective after continuous infusion. In rodents, BN3 also accelerated emergence from mechanistically distinct anesthetics, including etomidate, remimazolam, sodium {gamma} - hydroxybutyrate, midazolam, ketamine, sodium pentobarbital, and isoflurane. EEG recordings revealed a rapid cortical shift from slow-wave dominance to a wake-like high-frequency spectrum. Mechanistically, BN3 preferentially recruited ventral tegmental area (VTA) glutamatergic neurons: chemogenetic silencing abolished the BN3-evoked EEG spectral shift and strongly attenuated behavioral acceleration of emergence, whereas optogenetic activation of these neurons was sufficient to promote recovery. BN3 increased glutamate release in the nucleus accumbens and medial prefrontal cortex, and projection-specific inhibition of VTA[->]NAc or VTA[->]mPFC outputs blunted BN3-induced emergence. These findings define a VTA-centered glutamatergic arousal circuit that can be pharmacologically recruited as a common gateway for anesthetic-independent emergence.

neuroscience↗

bioRxiv2026

A novel uN2CpolyG Transgenic Mouse Model Recapitulates Multisystemic polyG Proteinopathy Pathology of Neuronal Intranuclear Inclusion Disease

Neuronal intranuclear inclusion disease (NIID) is a polyglycine disease that primarily affects the neuronal and neuromuscular systems. Here, we developed a novel transgenic mouse model that faithfully recapitulates the multisystemic impairments associated with polyG intranuclear inclusions. Our findings demonstrate that polyG expression induces neurodegeneration, behavioral deficits, and age-dependent accumulation of uN2CpolyG aggregates across multiple tissues.

animal behavior and cognition↗

bioRxiv2026

SWI/SNF nuclear foci scaffold peripheral gene hubs for circadian chromatin control

How dynamic circadian rhythms arise from a relatively static nuclear architecture remains a fundamental open question. Here, we identify the SWI/SNF chromatin-remodeling complex as a critical interface between the circadian clock and nuclear organization. Using endogenously tagged Moira (MOR), a core component of the Drosophila SWI/SNF complex and homolog of human BAF155, we find that MOR assembles into a small number of discrete foci near the nuclear periphery, in stark contrast to the current model of diffuse nuclear distribution for SWI/SNF-family proteins. We demonstrate that this localization is maintained by the inner nuclear envelope LEM-domain protein Otefin, effectively shifting MOR from a global to a localized regulator of chromatin architecture. DNA-FISH reveals that clock-regulated genes cluster into peripheral "hubs" that co-localize with MOR foci throughout the circadian cycle. ATAC-seq analysis shows that while MOR modulates chromatin accessibility genome-wide, it establishes a constitutive restrictive baseline specifically at clock-regulated loci. As a result, MOR depletion abolishes accessibility rhythms at these loci, rendering them constitutively hyper-accessible. This deregulation disrupts rhythmic gene expression and ultimately drives behavioral arrhythmia. Strikingly, oscillations of the core clock proteins PER and TIM remain intact, indicating that MOR loss uncouples the protein oscillator from its genomic output. Together, these results reveal that MOR-containing SWI/SNF foci form a stable perinuclear scaffold that gates chromatin accessibility, enabling the core clock machinery to convert transient protein oscillations into high-amplitude transcriptional rhythms. Significance StatementHow dynamic circadian rhythms emerge from a relatively static nuclear architecture remains a fundamental mystery. Here, we challenge the assumption that clock-target genes are randomly distributed by identifying a precise nuclear organization where these genes cluster into peripheral hubs. These hubs co-localize with stable SWI/SNF (MOR) foci anchored at the nuclear envelope. We demonstrate that this perinuclear scaffold is essential for gating rhythmic chromatin accessibility. Most importantly, loss of this architecture uncouples robustly oscillating clock protein program from its genomic and behavioral outputs. These findings reveal that circadian timekeeping is not merely a biochemical process but a spatially organized one, where nuclear topology licenses the translation of time into circadian rhythms.

cell biology↗

bioRxiv2026

Macrophage Antigen Presentation Is Unleashed by Pan-RAS Inhibition to Promote Antitumor Immunity

Pan-RAS inhibitors have emerged as potent targeted therapies designed to suppress oncogenic signaling in RAS-mutant tumors. However, whether these inhibitors possess therapeutic utility beyond tumors with intrinsic RAS dependency remains unclear. Here we show that the clinical-stage pan-RAS(ON) inhibitor RMC-6236 (Daraxonrasib) induces robust regression of NRAS-wild-type B16 tumors in immunocompetent mice, a response mediated by a mechanism independent of direct tumor-cell targeting. Instead, RMC-6236 acts by remodeling the tumor microenvironment, specifically enhancing the antigen-presenting capacity of tumor-associated macrophages through upregulated MHC-I expression. This anti-tumor efficacy is abrogated in T cell-deficient hosts, identifying a macrophage-dependent, T cell-mediated mechanism of control. Mechanistically, RMC-6236 does not directly block canonical RAS signaling in macrophages. Rather, it suppresses a Myc-Hdac2 epigenetic program, leading to enhanced histone H4 acetylation at the Nlrc5 locus and subsequent activation of the MHC-I master regulator NLRC5. Together, our findings reveal a macrophage-centered, epigenetically wired immune mechanism for pan-RAS inhibition that broadens the therapeutic scope of targeting the "undruggable" RAS pathway beyond tumor genotype towards systemic immune modulation.

immunology↗

bioRxiv2025

Mecp2 deficiency impairs microscale cortical network topology and dynamics in a Rett syndrome mouse model

Rett syndrome is a debilitating neurodevelopmental disorder with cerebral processing impairments caused by MECP2 loss-of-function mutations. Mecp2-deficient mouse models reveal disruptions of microscale cortical circuits. Yet how cellular-scale information processing is altered in Mecp2-deficient microscale functional networks is unknown. We investigated the development of functional connectivity, network topology, and dynamics in microelectrode array (MEA) recordings of primary cortical cultures from Mecp2-deficient and wild-type mice. Mecp2-deficient cortical networks developed more slowly and showed decreased functional connectivity compared to wild-type, leading to smaller network size, density, and strength of connectivity. Altered network topological features in Mecp2-deficient microscale circuits predicted decreased efficiency and information-sharing capacity. This reveals developmental deficits in microscale functional networks, which may in turn underlie the cortical decline and severe cognitive disability in Rett syndrome. These findings also offer circuit-level targets and an in-vitro approach for evaluating new therapeutic products for restoring microscale network function.

neuroscience↗

bioRxiv2025

Single-cell atlas reveals alveolar macrophage-specific Oncostatin-M drives pulmonary fibrosis via fibroblast activation in PCV2d infection

A hallmark of pulmonary fibrosis is the aberrant activation of lung fibroblasts into pathological fibroblasts that produce excessive extracellular matrix(1). Clarifying the cell-specific mechanisms by which viruses induce this process is crucial for developing effective strategies to intervene in disease progression. Here, we demonstrate that alveolar macrophage subsets specifically express tumor suppressor M (Osm) after infection by PCV2d infection and related intervention experiments in mice, combined with single-cell transcriptome sequencing (scRNA-seq). Through validation using histopathological analyses and an in vitro macrophage-fibroblast co-culture model, these alveolar macrophage-derived oncostatin M (Osm) were confirmed to specifically drive fibroblast activation. Vaccine intervention experiments further confirmed that targeted inhibition of oncostatin M (Osm) expression in alveolar macrophages significantly attenuated fibroblast activation and extracellular matrix deposition, thereby mitigating pulmonary fibrosis progression. Therefore, subgroup-specific secretion of oncostatin M (Osm) by alveolar macrophages represents a key driver mediating PCV2d infection-induced pulmonary fibrosis, and targeting this pathway offers a potential therapeutic strategy for viral-induced pulmonary fibrosis.

genomics↗

bioRxiv2025

Dynamic alterations of DNA methylation and transcriptome in adaptation to and recovery from the space environment

Space exploration presents tremendous health challenges. Here, we report time series of multi-omic and phenotypic profiles of seventeen astronauts from six China Manned Space missions with continuous spaceflight durations ranging from 13 to 180 days. We revealed a key role of DNA methylation regulation in reshaping gene expression patterns to adapt to the space environment. Long-duration spaceflight showed more alterations in epigenetic modifications correlated with alternative splicing and protein acetylation. During recovery, an "overrange rebound" phenomenon was observed, furthermore, a mathematical model was established to describe this implying important phenomenon. Moreover, we revealed the correlations between molecular alterations and phenotypic changes such as coagulation activation and bone intensity loss. Additionally, we performed ground-based simulation experiments to estimate the impacts of individual stressors in the space environment on DNA methylation. In summary, our study highlights the importance and complexity of epigenetic regulation in adaptation to and recovery from the space environment.

genomics↗

bioRxiv2025

ABA-responsive transcription factor CbNAC63 is involved in modulating biosynthesis of triterpenoid saponins in Conyza blinii

Conyza blinii, a traditional Chinese medicinal herb, accumulates triterpenoid saponins. NAC transcription factors (TFs) are pivotal for plant stress responses and hormone-mediated secondary metabolism, while abscisic acid (ABA) regulates terpenoid biosynthesis in medicinal plants. However, how NAC TFs mediate ABA-regulated triterpenoid saponin synthesis in C. blinii remains unclear. In order to address this gap, the focus was directed towards CbNAC63--a NAC TF identified from the nocturnal low-temperature transcriptome of C. blinii. Phylogenetic and motif analyses showed it belongs to the stress-responsive NAC subclade with conserved domains. Y2H assays revealed its self-interaction, enhancing transcriptional activity; subcellular localization confirmed nuclear localization. RT-qPCR results indicated CbNAC63 exhibits tissue-specific expression under nocturnal low-temperature stress, accompanied by increased triterpenoid saponin accumulation. ABA signaling primarily regulates this process: exogenous ABA enhanced CbNAC63 expression and saponin content, while fluridone suppressed both. Overexpression (OE) and virus-induced gene silencing (VIGS) demonstrated CbNAC63 positively regulates saponin biosynthesis. Y1H and dual-luciferase reporter assays confirmed CbNAC63 directly binds to the promoters of Cb{beta}AS and CbHMGR and activates their transcription. In summary, the study shows CbNAC63 integrates ABA and low-temperature signals, activating MVA pathway genes to regulate saponin synthesis. This unveils a novel "ABA-CbNAC63-MVA" module, enriches the classic regulatory network, and provides a target for improving medicinal plant quality. HighlightsIdentifies CbNAC63 as a novel regulator that integrates ABA and cold signals to boost saponin production in medicinal plants.

plant biology↗

bioRxiv2025

Deconvolution of Sparse-count RNA Sequencing Data for Tumor Cells Using Embedded Negative Binomial Distributions

Estimating tumor-specific transcript proportions from mixed bulk samples has potential to inform novel biology. However, estimation accuracy using existing methods in sparse-count data such as microRNA-seq and spatial transcriptomics has yet to be established. We generated a mixed small RNA benchmark dataset to demonstrate analytical challenges. To resolve them, we developed DeMixNB, a semi-reference-based deconvolution model assuming a sum of negative binomial distributions. Applications to miRNA-seq from 856 patients with breast cancer and 3,755 spatial spots from lung cancer generated either clinical or mechanistic insights into tumor cell plasticity. This supports the important utility of DeMixNB to investigate cancer RNomes.

bioinformatics↗

bioRxiv2025

A wild genome of the underutilized legume lablab (Lablab purpureus) reveals the genetic basis of domestication

BackgroundWith global food security threatened by climate change and the growing global population, underutilized crops offer sustainable solutions for diversifying current agricultural systems. Lablab (Lablab purpureus) is a highly versatile, climate-resilient underutilized legume native to Africa and widely, but locally, cultivated in Asia with untapped potential for sustainable agriculture. However, the lack of wild genome resource prevents a comprehensive genome utilization research for this underutilized crop. This paper presents the first chromosome-scale genome of wild lablab with its complete gene annotation and provides comprehensive population genomic analyses of its evolution and domestication by resequencing a panel of wild and domesticated accessions. ResultsThe genome was assembled into a total size of 478.2 Mb with a scaffold N50 of 39.7 Mb, and 96.4% (460.8 Mb) of the scaffolds anchored to 11 pseudochromosomes, the haploid chromosome number of lablab. We demonstrated that domestication was likely in Africa with several subsequent instances of transportation into Asia. Our analyses identified selective sweeps resulting from domestication as well as pseudogenes associated with yield-related traits and stress tolerance, representing candidate genes for further validation and targets for future breeding programs. ConclusionsOur genomic resource for wild lablab delineated its domestication history and identified key genes and pseudogenes under selection, bridging the gap between its untapped wild diversity and breeding for improved stress resilience and yield in underutilized legumes. This offers genomic and genetic insights for crop improvement of lablab.

evolutionary biology↗

bioRxiv2025

Sequestration of clock proteins into repressive nuclear condensates orchestrates circadian gene repression

Circadian clocks orchestrate [~]24-hour cycles in gene expression, behavior, and physiology across most organisms1. Our recent study has revealed a striking spatial organization in the nucleus during the repression phase: core clock proteins such as Drosophila PERIOD (PER) are organized into distinct nuclear foci close to the inner nuclear envelope of clock neurons, and clock-regulated genes are similarly positioned in the nucleus2. However, the functional relevance of this subnuclear organization is unknown. Here, we investigate how the spatial organization of clock proteins and chromatin regulates circadian gene repression. Given that PER partners with TIMELESS (TIM) to enact transcriptional repression, we first investigated whether TIM is also a component of these nuclear foci. Using CRISPR-Cas9 to endogenously tag TIM with mNeonGreen, we performed high-resolution live imaging in Drosophila clock neurons. We found that TIM forms nuclear foci during the repression phase that co-localize with PER condensates, whereas TIM remains diffuse in the cytoplasm of per01 null mutants. To probe the spatial relationship between these condensates and clock-regulated genes, we combined protein imaging with fluorescence in situ hybridization (FISH) which revealed that PER/TIM condensates were positioned adjacent to, but did not overlap with, clock gene loci during the repression phase. These results suggest that core clock proteins are spatially sequestered into repressive condensates away from chromatin, providing a new framework for understanding how nuclear architecture and phase separation together orchestrate rhythmic gene expression.

cell biology↗

bioRxiv2025

An intron-based timer for circadian rhythms

Abstract: Circadian clocks regulate daily rhythms in all eukaryotes through [~]24-hour transcriptional-translational feedback loops driven by clock proteins. However, the molecular mechanisms that set the 24-hour period remain poorly defined. Here, using single-molecule imaging and nascent RNA sequencing, we uncover an unexpected RNA-based molecular timer: a single intron in the Drosophila timeless (tim) gene that regulates circadian period length by controlling mRNA localization. Strikingly, we find that [~]50% of tim mRNAs are localized to the nucleus due to inefficient post-transcriptional splicing of a single intron (which we named intron P), in contrast to other core clock transcripts that localize predominantly to the cytoplasm. CRISPR-mediated removal of intron P abolishes nuclear retention of tim transcripts, leading to accelerated TIM protein accumulation and a shortened [~]22-hour period with reduced rhythmic robustness. Remarkably, insertion of intron P alone into heterologous reporters is sufficient to promote nuclear retention in both Drosophila and human cells, acting as a conserved checkpoint that withholds transcripts in the nucleus until splicing is complete. Finally, we identify three RNA-binding proteins, two repressors (Hrb27C and Squid) and one activator (Qkr58E-2, a Sam68 homolog), that modulate intron P splicing in a rheostat-like manner. Together, these findings establish tim intron P as the first intron-based molecular timer in circadian clocks and reveal splicing kinetics as a critical regulatory layer in temporal gene expression programs, with broad implications for other processes such as development and immunity.

molecular biology↗

bioRxiv2025

Open Raman Microscopy (ORM): A Modular Hardware and Software Framework for Accessible Raman Imaging

Raman microscopy is a label-free, non-destructive imaging tool for spatially resolved chemical fingerprinting. Its powerful ability to reveal molecular information has driven rapid growth in applications across fields as varied as materials science, environmental analysis, and biomedical research. Despite its versatility, the accessibility of Raman microscopy is limited by expensive commercial setups and the technical barriers faced by researchers attempting to build custom systems. Here, we introduce an Open Raman Microscopy (ORM) framework based on a readily accessible modular microscopy platform. The ORM platform provides configurations for both high-throughput imaging and confocal imaging. We developed a dedicated python-based control and acquisition software, the ORM-Integrated Raman and Imaging Software (ORM-IRIS) designed to accommodate modular integration and control of components, including the laser source, spectrometer, and translational stages. Implemented across three institutions we demonstrate the ORM platform for high-throughput imaging of articular cartilage tissue, confocal three-dimensional imaging of a zebrafish embryo, and imaging of gold colloid decorated surfaces for surface enhanced Raman spectroscopy. Together, this open-source hardware and software framework enhances the accessibility of Raman microscopy across an expanding range of scientific applications.

biophysics↗

bioRxiv2025

AAV-mediated CSNK2B gene replacement rescues ASD-relevant phenotypes and establishes EEG biomarkers for translation in Csnk2b haploinsufficient mice

De novo CSNK2B variants are strongly associated with autism spectrum disorder (ASD) and early-onset epilepsy, yet in vivo therapeutic evidence and translatable biomarkers remain limited. We generated Csnk2b haploinsufficient (Csnk2b+/-) mice that recapitulate core clinical features--ASD-like social and cognitive deficits, heightened anxiety, spontaneous seizures, cortical and hippocampal structural compromise, and reduced PV-interneuron density with impaired cortical inhibition. Neonatal brain-wide AAV-PHP.eB-mediated CSNK2B replacement (hsyn or CAG promoters, retro-orbital P3) restored cortical/hippocampal structure, normalized neuronal numbers, prolonged survival, and ameliorated seizures and ASD-like behaviors with comparable efficacy across promoters. Critically, treatment also corrected quantitative EEG signatures that are directly deployable in human trials: theta and gamma band power were normalized, theta/gamma (and beta/gamma) ratios recovered, and inter-areal coherence and gamma-band effective connectivity were restored, indicating re-established excitation/inhibition balance and large-scale network coordination. These EEG endpoints constitute a compact, noninvasive biomarker panel of target engagement and physiological efficacy that can be harmonized with clinical EEG to support dose finding, early decision-making, and longitudinal monitoring in CSNK2B gene-therapy trials. Together, our data provide preclinical proof-of-concept that early AAV-mediated CSNK2B replacement is therapeutically effective and nominate band-limited EEG metrics as translational readouts to accelerate first-in-human studies for CSNK2B-linked neurodevelopmental disorders.

neuroscience↗

bioRxiv2025

StrucTrace: Fourier Watermarking for Traceable Bio-molecular Assets

The rise of generative artificial intelligence (GenAI) in protein and nucleic acid design has created unprecedented opportunities for synthetic biology, but also heightened the need for reliable provenance and intellectual-property protection. To meet this challenge, we present a Fourier domain watermarking framework that encodes digital identifiers directly into three-dimensional biomolecular structures. By perturbing only flexible backbone atoms and embedding information through frequency domain modulation, the method achieves imperceptible alterations while ensuring deterministic and reversible decoding. Large-scale validation on over 40,000 protein structures demonstrates its robustness: structural deviations remain orders of magnitude below biological thresholds, watermarks are recovered with perfect accuracy, and functional analyses confirm stability at both thermodynamic and dynamic levels. Beyond technical performance, the approach provides a foundation for a broader ecosystem of secure biomolecular asset management, integrating provenance verification, access control, and digital rights management. Together, these advances establish biomolecules as traceable and auditable digital assets, aligning the future of bio-design with emerging standards for trustworthy AI.

bioinformatics↗