Biology subjects

Wei, X.

Publications and source records attributed to Wei, X..

At least 37 records · Page 2Linked to original sources

bioRxiv2026

Palmitoylation calibrates mitochondrial transport of insulin across the endothelium in insulin resistance

Impaired insulin transport across the endothelium contributes to insulin resistance, a poorly understood condition implicated in diabetes and many other chronic diseases. Insulin has been reported to undergo non-receptor-mediated endocytosis resembling fluid-phase uptake through unclear mechanisms. Here we show in mice with diet-induced insulin resistance that endothelial-specific deletion of the depalmitoylase acyl-protein thioesterase 1 (APT1) improved glucose tolerance and insulin sensitivity without affecting chronic inflammation or capillary structure. Endothelial APT1 deficiency increased interstitial insulin levels in mice confirmed by in-situ microneedle-based sampling. In cultured human microvascular cells, APT1 inhibition enhanced cell transport of high-dose insulin independent of the insulin receptor and canonical endocytic machinery. Unexpectedly, live-cell imaging revealed insulin rapidly localizing to mitochondria prior to endolysosomal trafficking, even at physiological insulin concentrations. APT1 inhibition delayed mitochondrial discharge of insulin to lysosomes. Cyclosporin A, an immunosuppressant known to affect mitochondrial function, preserved mitochondrial insulin content and promoted insulin transport in cultured cells, and enhanced interstitial insulin delivery in mice. Proteomic analysis revealed two palmitoylated proteins, PACS1 and YTHDF2, required for APT1-mediated mitochondrial-endolysosomal trafficking of insulin. A mitochondrial insulin shuttle in endothelial cells may participate in the physiological adaptation to hyperinsulinemia and its regulation by palmitoylation suggests a novel approach to insulin resistance.

physiology↗

bioRxiv2026

Systematic Development of a Compact Genome-Editing Tool Leveraging the TAM-Independent DNA Nuclease TasR in Bacillus subtilis

Bacillus subtilis is a core microbial chassis in biomanufacturing, and establishing efficient gene editing technologies is key to engineering this strain. In conventional CRISPR gene editing technologies, the large size of DNA nucleases leads to difficulties in plasmid construction, low transformation efficiency, and cumbersome multi-round editing operations; therefore, developing miniature gene editing tools can effectively address these issues. Although our group previously established a miniature gene editing tool based on IscB in B. subtilis SCK6, IscB relies on the 5'-CAGGAA-3' TAM recognition sequence, and 83.36% of the genes in the SCK6 genome harbor no or only one TAM sequence, indicating a bottleneck of restricted editing for IscB in this strain. The novel miniature DNA nuclease TasR does not require a TAM sequence and can thus compensate for the limitation of IscB; however, the applicability of TasR in B. subtilis remains unknown. Therefore, this study first constructed a single plasmid, pBsuTasR, capable of expressing TasR and its guide RNA (tigRNA), which enabled gene deletion of regular-sized fragments in SCK6 with editing efficiencies of 21.7%- 78.3%. Subsequently, the capacity of TasR to delete a long DNA fragment (169.9 kb) was evaluated, and it was found that under the guidance of a single tigRNA, the deletion efficiency was 21.73%, whereas after optimizing to two tigRNAs, the efficiency increased to 39.13%. Furthermore, the gene integration capability of pBsuTasR was further tested, and TasR was able to integrate the aprN gene into the amyE locus at an efficiency of 13.3% under the guidance of a single tigRNA, and after increasing to two tigRNAs, the integration efficiency increased to 91.3%. In terms of iterative genome editing, this study developed the pBsu-SRP (Scissors-Rock-Paper) iterative editing system, which automatically cures the editing plasmid from the previous round while performing a new round of gene editing, with sequential gene deletion efficiencies of 4.34%-26.08%, and using this system, the editing cycle can be shortened from 4N days by the conventional method to 3N+1 days. Subsequently, the pBsu-SRP system was successfully used to achieve the integration of two and three copies of the mCherry fluorescent reporter gene in SCK6, and it was found that the fluorescence intensity increased with the copy number. Finally, this study also explored the escape of SCK6 from TasR cleavage and found that mutations in the tigRNA sequence are the cause of the escape. In summary, this study constructed a novel miniature genome editing system in B. subtilis using the TAM-independent nuclease TasR as the core component. This system can not only provide an efficient technical tool for genetic manipulation of industrial microorganisms, but also offer new instrumental support for the iterative engineering and functional optimization of chassis cells in biomanufacturing.

molecular biology↗

bioRxiv2026

Mechanism of fatty acid uptake and inhibition in human FATP2

Fatty Acid Transport Protein 2 (FATP2) couples fatty acid uptake to intracellular activation and is associated with pathological lipid accumulation in cancer and nonalcoholic fatty liver disease. Here, we present cryo-electron microscopy structures of human FATP2 across its reaction cycle. Our structures suggest that FATP2 recruits fatty acids directly from the membrane interface through a hydrophobic tunnel. Catalysis involves a [~]130{degrees} rotation of the C-terminal domain, a transition trapped by the antihypertensive drugs isradipine and benidipine. Both drugs lock the enzyme in a thioester-forming state, but benidipine exhibits superior efficacy by extending a bulky moiety into the primary catalytic tunnel to sterically block substrate entry. Furthermore, we identify a product inhibition mechanism where excess acyl-CoA traps the enzyme, potentially limiting metabolic overload. These findings provide a structural framework for understanding vectorial fatty acid channeling and a scaffold for developing modulators of metabolic flux. HighlightsO_LICryo-EM structures of human FATP2 reveal a membrane-anchored lollipop topology C_LIO_LIEndogenous fatty acids within a hydrophobic tunnel delineate the fatty acid uptake pathway C_LIO_LIIsradipine and benidipine displace fatty acids to trap a non-productive conformation C_LIO_LIAcyl-CoA product inhibition may provide negative feedback via steric occlusion C_LI

biophysics↗

bioRxiv2026

Fast and Accurate Photon-Transport Modeling based on Foundation-Model-Encoded Implicit Neural Surrogate towards Optimized Near-Infrared Brain Stimulation

Clinical treatment planning for near-infrared (NIR) neuromodulation requires patient-specific dosimetry to optimize light fluence (LF) delivery to cortical targets. The gold-standard Monte Carlo photon-transport forward solver is accurate but computationally expensive and non-differentiable for personalized inverse design across subjects. Here, we present PhomiNeuro, a foundation-model-encoded differentiable surrogate for time-resolved LF modeling and pathology-guided inverse design. A pretrained 3D medical imaging foundation model (VISTA3D) was domain-adapted to 285 training head models annotated with optical properties, and then coupled to an implicit neural representation (INR) that predicts LF at arbitrary spatiotemporal coordinates. Regularized by a time-dependent diffusion-equation residual, it demonstrated superior fidelity in 84 held-out participants, and ablations identified VISTA3D-derived anatomical priors as dominant and physics regularization as complementary. PhomiNeuro enables fast and robust queries of LF and its gradients with respect to illumination parameters for targets guided by individual structural magnetic resonance imaging and amyloid positron emission tomography, achieving 466-fold per-iteration speedup and 167-fold end-to-end optimization speedup. Explanatory analyses of LF delivery variability, including sex differences and amyloid status, identified structural variations as the primary drivers. These results position PhomiNeuro as a highly extensible translational framework toward personalized treatment planning and digital twin development in precision neuromodulation.

bioengineering↗

bioRxiv2026

Ancient pyroptotic machinery via GSDMA/B cleavage by LPS-activated caspase-1 in cartilaginous fish

Gasdermins are pore-forming effectors that mediate pyroptosis, an inflammatory form of programmed cell death characterized by membrane permeabilization and the release of intracellular contents. Phylogenetically, gasdermin members can be broadly divided into two major branches, the GSDME/PJVK branch and the GSDMA/B/C/D branch. Whereas the GSDME mediated pyroptosis was traced back to metazoans, the functional origins of GSDMA/B/C/D branch remain poorly understood. As a basal representative of the GSDMA-D lineage in cartilaginous fish, Callorhinchus milii GSDMA/B (CmiGSDMA/B) provides essential information for the ancestral state of this branch. Here, we functionally characterized CmiGSDMA/B and identified CmiCASP1 as its upstream protease. Mechanistically, Lipopolysaccharide (LPS) activates CmiCASP1 via its CARD domain, leading to cleavage of CmiGSDMA/B into two functionally distinct products, N241 and N288. N241 binds cell membrane to drive pyroptosis, whereas N288 suppresses N241-triggered cell death. Interestingly, N241 exhibits bactericidal activity against Gram-negative bacteria in vitro, suggesting that antimicrobial activity may have been an early feature of the GSDMA-D lineage. Collectively, these findings provide insight into a non-canonical, LPS-responsive, caspase-driven pyroptosis pathway in cartilaginous fish and reveal the dual-fragment antagonistic regulation within this branch.

evolutionary biology↗

bioRxiv2026

Transcriptional plasticity of ventral tegmental area neurons induced after cessation of chronic cocaine exposure is required for incubation of cocaine seeking

Chronic cocaine triggers changes in brain function that persist long after drug taking has ceased. Relapse to substance use during abstinence can be triggered by drug-associated cues, implicating the drug-free period after chronic cocaine as a time when the probability of relapse is modulated by plasticity mechanisms. Here, we studied the regulation and function of transcriptional plasticity activated in a time-dependent manner in dopaminergic and glutamatergic neurons of the mouse ventral tegmental area (VTA) over a drug-free period after chronic cocaine. We used in vivo dCas9/CRISPR inhibition to demonstrate a causal role for Brain-Derived Neurotrophic Factor transcription in the incubation of cocaine seeking during abstinence, and we used single-nucleus sequencing to identify a program of gene regulation induced in VTA neurons selectively by the prolonged absence of cocaine. These data advance the understanding of plasticity mechanisms that modulate reward functions of VTA neurons, which may be a main factor propagating relapse in substance use disorders.

neuroscience↗

bioRxiv2026

Structural assemblies for an RNA world

Protein homo-oligomerization widely generates symmetric assemblies for encapsulation and scaffolding. Conversely, natural RNA quaternary structures appear limited, with known RNA-only multimers predominantly forming dimers or dihedral assemblies from long transcripts. Whether short RNAs can access broader higher-order assembly space has remained unclear. Here, using cryo-EM, we show that RNAs under 200 nucleotides form three distinct structural classes: a 60-subunit viral-capsid-like icosahedron, non-caged oligomers including a trimer and a strand-exchanged dimer, and a continuous filament assembled from a 57-nucleotide RNA. These structures demonstrate that assembly complexity does not simply scale with RNA length; compact RNAs can specify architectures traditionally associated with proteins. Our findings broaden the known RNA quaternary repertoire, strengthen the structural plausibility of higher-order organization in an RNA world, and establish foundational reference architectures to guide future RNA-based self-assembling nanoparticle design. HighlightsO_LIShort RNAs reveal protein-like assembly principles for an RNA world C_LIO_LIThe first natural RNA-only T=1 icosahedral cage is a viral-capsid-like 60-mer C_LIO_LICompact RNA-RNA interfaces encode global curvature, valency and propagation C_LIO_LIRNA motifs assemble into closed cages, finite oligomers and extended filaments C_LI

evolutionary biology↗

bioRxiv2026

PlantGeneAnn: a strand-specific genome foundation model for ab initio gene structure annotation of plant genomes

High-quality plant genome assemblies are rapidly increasing, but accurate structural annotation remains reliant on transcript and homology evidence, limiting applications in newly sequenced and non-model species. Here, we present PlantGeneAnn, a plant-optimized, strand-specific genome foundation model for ab initio gene structure annotation. Fine-tuned on only nine high-quality model plant annotations, PlantGeneAnn outperformed a multi-species model trained on 42 species, showing that annotation quality is more important than token volume. On a stringent 13-species benchmark covering rosids, asterids, and monocots, PlantGeneAnn surpassed four state-of-the-art baselines across five evaluation levels, from base-level classification to complete transcript recovery. It achieved higher intron precision and better captured complex gene structures. In zero-shot variant effect prediction, PlantGeneAnn identified cryptic splice donors and premature stop codons in maize and rice, with saturation mutagenesis confirming single-nucleotide, context-dependent sensitivity. It also retained generalizability for epigenomic track prediction, highlighting its value for pan-genomics, crop improvement, and non-model plant research.

bioinformatics↗

bioRxiv2026

Targeting Cellular Pseudo-Senescence to Overcome PARP inhibitors Resistance in BRCA1 -Mutated Breast Cancer

Poly (ADP-ribose) polymerase (PARP) inhibitors (PARPi) are a mainstay therapy for homologous recombination (HR)-deficient cancers; however, resistance remains a major clinical challenge. Previously, through a genome wide CRISPR screen, we identified ZNF251 haploinsufficiency as a novel driver of PARPi resistance. In BRCA1-mutant (BRCA1mut) cells, ZNF251 deficiency led to HR hyperactivation, conferring PARPi resistance that could be reversed by RAD51 inhibition. In this study, we further show that ZNF251 deficiency induces replication stress and a pseudo-senescence state, in which cells exhibit molecular and phenotypic markers of senescence while retaining proliferative capacity. Because senomorphic and senolytic therapies can target senescent cells, we tested whether these approaches could overcome PARPi resistance in ZNF251-deficient breast cancer cells. Critically, targeting this senescence-like state with either senomorphic agents, such as cytokine inhibitors, or senolytic agents, such as BCL-2 and BCL-XL inhibitors, overcame PARPi resistance ex vivo and in vivo. Importantly, pseudo-senescence was also observed in other PARPi-resistant contexts driven by HR hyperactivation, including 53BP1- and Shieldin-mutant cells, suggesting that it may represent a broader mechanism underlying PARPi resistance in breast cancer. Furthermore, in two olaparib-resistant, BRCA-mutant triple-negative breast cancer organoid models, treatment with DT2216, a BCL-XL-targeting PROTAC, sensitized both models to olaparib. Together, our work defines a novel pathway linking HR hyperactivation, replication stress, and pseudo-senescence, and positions both senomorphic and senolytic therapies as promising strategies to overcome PARPi resistance in BRCA1mut breast cancer. HighlightsO_LIZNF251 deficiency drives PARP inhibitor resistance through HR hyperactivation, replication stress, and pseudo-senescence in BRCA1-mutant breast cancer. C_LIO_LISenomorphic and senolytic therapies overcome PARP inhibitor resistance in vitro, in vivo, and in patient-derived organoid models. C_LIO_LIPseudo-senescence represents a shared vulnerability of HR-hyperactivated PARPi-resistant cancers and can be therapeutically targeted. C_LI

Cancer Biology↗

bioRxiv2026

The Logic of Thalamic Inputs onto the Molecular Taxonomy of Cortical Neurons Reveals a Visual Hierarchy

The hierarchical organization of sensory cortices and the rich molecular taxonomy of their cell types are defining features of the mammalian cortex. Cortical areas along this hierarchy are reciprocally connected via the thalamus through bottom-up and top-down projections. The logic through which these projections map onto the cellular taxonomy of the cortex is, however, poorly understood. Here we combine an anterograde transsynaptic tracer with spatial transcriptomics to reveal the molecular and spatial identity of mouse visual cortical neurons downstream of thalamic starter neurons across visual cortical areas. Distinct thalamic inputs target characteristic sets of molecularly defined cortical neurons, forming bottom-up or top-down "signatures" defined by cell-type composition and the ratio of GABAergic to glutamatergic neurons. These signatures reveal a hierarchy spanning thalamic nuclei and visual cortical areas, independently predicted by the molecular and cellular similarities between cortical areas. This work uncovers basic principles of how bottom-up and top-down thalamic inputs map onto the cellular taxonomy in the visual cortex and establishes a cellular framework for the cortical hierarchy.

neuroscience↗

bioRxiv2026

Distance Mapping and Variable-Specific Geometry of Goal-Relevant Frames in the Retrosplenial Cortex

Goal-directed navigation requires animals to continuously update their position relative to an unmarked goal. Here, we recorded retrosplenial cortex (RSC) activity in freely moving rats during goal-directed navigation and random foraging. We found that RSC neurons encoded the Euclidean distance to the goal, and that this distance representation was selectively biased toward the goal during navigation. This goal-biased signal could not be explained by non-uniform behavioral sampling alone. Task engagement selectively enhanced allocentric head-direction representations anchored to a landmark cue, whereas egocentric boundarybearing signals showed no detectable task-related enhancement and no detectable goalcentered spatial organization in this task context. Mixed-selective RSC population activity further exhibited variable-specific separability-smoothness geometry: distance-to-goal showed high local smoothness and decoding performance, whereas egocentric boundary bearing showed stronger macro-scale separability. These task-related spatial representations persisted under reduced visual input, suggesting contributions from memory and self-motion signals. Together, these findings indicate that RSC organizes goal-relevant spatial representations in a task-dependent manner.

neuroscience↗

bioRxiv2026

Characterization of pre-analytical blood collection and stabilization parameters to maintain endogenous protein levels for remote blood sampling technology

Blood biomarkers are central to monitoring disease progression and evaluating treatment responses, yet traditional venipuncture captures a single physiological snapshot in time and becomes burdensome with repeated sampling. Remote blood self-sampling offers a path toward longitudinal, decentralized monitoring, but maintaining protein integrity from draw to analysis remains a critical challenge. Here, we optimized pre-analytical blood collection and stabilization parameters to maintain protein levels at the time of collection for use with remote sampling technology. First, we optimized blood collection time with Tasso remote self-sampling devices to minimize interference from clotting, finding that a 2.5 min collection time best reduces clot formation while collecting enough blood. Next, we found that Protein Plus, a commercial protein stabilizer, limited hemolysis (a metric for stabilizer efficacy) in venous blood for up to 5 days at 25{degrees}C-35{degrees}C and for 1 day at 40{degrees}C. In addition, we optimized the stabilizer volume and acceptable blood volume range for self-sampling as the stabilizer efficacy is impacted by the stabilizer to blood ratio and collection volume can vary with remote self-sampling devices. Finally, we incubated stabilized blood samples collected via Tasso device at 25{degrees}C-35{degrees}C for 72 h, mimicking a 2-day shipping period. Using a panel of 21 inflammatory proteins, we found that Protein Plus limited intracellular protein release for various proteins (e.g., VEGF-A, CCL11, and IL-8), inhibited protein degradation for CCL2, and enabled minimal hemolysis. These results support Protein Plus as a viable stabilization strategy for remote blood collection technology targeting longitudinal inflammatory protein monitoring.

biochemistry↗

bioRxiv2026

SpatialClaw: A Memory-Augmented Autonomous Ecosystem for Spatial Omics Analysis

While the expansion of spatial omics has revolutionized our ability to dissect tissue architecture, the accumulation of incompatible computational methods has heavily fragmented end-to-end analysis, rendering complex workflows irreproducible. Generic conversational agents lack the domain-specific precision necessary to navigate the intricate biological pipelines. To overcome this, we present SpatialClaw, a memory-augmented autonomous ecosystem to unify spatial omics analysis under a single natural-language interaction. SpatialClaw integrates 30 specialized skills, spanning raw data preprocessing, spatial domain identification, deconvolution, spatially variable gene detection, cell-cell communication analysis, multi-sample and cross-modality integration. Distinct from existing agents, SpatialClaw introduces a graph-based persistent memory architecture that stores dataset metadata, analysis lineage, biological insights, and user preferences as versioned nodes and edges across three hierarchical layers (Session, Episodic, and Semantic), governed by a deterministic promotion policy. A Memory-Augmented Reasoning (MAR) Operator bridges the memory store and the main agent, synthesizing retrieved experiences into task-specific guidance for each query. In rigorous benchmarking spanning three memory-sensitive scenarios across 10 spatialomics skills, SpatialClaw outperforms both a standard large language model and the memory-only configuration. Furthermore, we demonstrate its robust biological utility by dissecting the complex tumor microenvironment of a 15-section human triple-negative breast cancer cohort. In merely three conversational turns and with zero direct scripting, SpatialClaw executes a comprehensive end-to-end workflow, yielding standardized output bundles. Ultimately, by synergizing comprehensive analytical tools with structured persistent memory, SpatialClaw elevates spatial omics from disjointed computational stitching to a fully traceable, reproducible, and self-improving discovery ecosystem. SpatialClaw is ready to use at https://github.com/ShangBioLab/SpatialClaw.

bioinformatics↗

bioRxiv2026

Cell Type-informed Characterization of Spatial Niches from Spatial Multimodal and Multi-omics Data

Cell niches play critical roles in tissue organization and orchestrate homeostasis, development, and disease progression. Advances in spatial omics technologies now allow diverse molecular and image-derived data to be jointly captured while preserving spatial context, but deciphering cell niches from such spatial multimodal and multi-omics data remains challenging. Existing computational methods are still limited in their flexibility across variable combinations of spatial modalities and omics data. Here we introduce SpaNECT, a unified and flexible framework designed to accommodate spatial multimodal and multi-omics data for cell niche characterization. SpaNECT further incorporates reference-informed cell-type information to support biologically interpretable niche analysis. Systematic evaluations across diverse tissues, disease conditions, and developmental stages showed that SpaNECT consistently outperformed representative methods in resolving cell niches. In mouse brain spatial multi-omics data, SpaNECT uncovered niche-associated molecular and regulatory programs; in developing chick heart, it tracked cross-stage niche reorganization and progressive remodeling of ventricular-associated cell states during maturation. Overall, SpaNECT establishes a general and robust framework for characterizing cell niches across spatial multimodal and multi-omics data.

bioinformatics↗

bioRxiv2026

Pathway-informed Universal Domain Adaptation for Single-cell RNA-seq Data

The rapid accumulation of single-cell atlases has yielded datasets of unprecedented scale, encompassing samples across diverse platforms, locations and laboratories. This multidimensional complexity drives an urgent need for universal domain adaptation methods capable of achieving precise cell-type annotation. However, existing methods lack computational scalability and fail to integrate biological priors. Here, we develop scPathOT, a pathway-informed universal domain adaptation framework that leverages pathway activation transformations to harmonize single-cell datasets across disparate conditions. We demonstrate the versatility of scPathOT across diverse technological platforms, tissues, disease contexts, cellular senescence and treatment conditions. Crucially, this pathway-informed alignment not only accurately resolves cellular identities but also uncovers functional mechanism. In pancreatic islets, scPathOT delineates a shared stress-repair axis traversed by {beta}-cells prior to their divergence into type 1 and type 2 diabetes-specific states. In aging bone marrow, scPathOT disentangles lineage-specific senescence modules that unexpectedly converge onto unified inflammatory and oxidative-stress programs. Furthermore, application to an in-house pancreatic ductal adenocarcinoma cohort uncovers the mechanistic basis underlying the neoadjuvant chemotherapy-induced reorganization of stromal-immune crosstalk. By coupling biological priors with universal domain adaptation, scPathOT provides a scalable, mechanistically interpretable framework to accelerate biological discovery from atlas-level single-cell data.

bioinformatics↗

bioRxiv2026

ExMODE: A Multi-Omics Repository for Extremophile Adaptation and Bioprospecting

Extreme environments, though hostile to most life forms, host specialized extremophile communities that have redefined biological cognition and emerged as vital biotechnological resources, with their unique adaptive traits and bioactive molecules driving advances in multiple scientific and industrial fields. However, research on extremophiles is hindered by limitations in culture-based methods, fragmented multi-omics data with non-uniform annotation standards across repositories, the lack of cross-extreme comparative research in existing resources, and the singularity of data dimensionality that neglects key structural information, all of which restrict the functional interpretation of extremophile microbes and the exploitation of their bioprospecting potential. To tackle these challenges, we developed ExMODE (https://db.genomics.cn/exmode/), a comprehensive multi-omics database platform dedicated to extremophiles. It centrally integrates multi-omics data from diverse extreme habitats with a standardized annotation framework, resolving data fragmentation and enabling systematic cross-environment comparative analyses to elucidate extremophile adaptive mechanisms. Moreover, ExMODE aggregates multi-dimensional datasets including genes, genomes, secondary metabolite sequences and protein structures, overcoming the constraints of single-dimensional data and significantly improving the efficiency of biotechnological resource discovery from extreme microorganisms.

microbiology↗

bioRxiv2026

H2A.Z levels control the timing of major events at the maternal-zygotic transition

Across animals, early embryonic events are temporally tightly coordinated but the underlying mechanisms remain incompletely understood. In Drosophila, both global and nuclear levels of the histone variant H2Av rise progressively during the maternal-zygotic transition (MZT), but whether this increase is functionally important is unknown. We find that increased H2Av dosage expedites specific MZT events: the transition from nuclear cycle (NC) 13 to 14 occurs prematurely as does the turnover of thousands of maternal transcripts; in addition, a subset of genes is precociously expressed in the zygote. Reduced H2Av dosage has reciprocal effects. Comparable transcriptional shifts are observed in zebrafish embryos overexpressing the H2Av ortholog H2A.Z, suggesting H2Av/H2A.Z dosage as a conserved timer of early development. We also examined mutants with impaired H2Av sequestration on lipid droplets which exhibit increased nuclear H2Av levels but reduced cytoplasmic levels. Unexpectedly, nuclear H2Av abundance influences the timing of NC 13 but is not the main driver of transcriptome remodeling. In summary, we find that H2Av/H2A.Z levels are critical timers of early embryogenesis and that H2Av can act in part via a non-nuclear mechanism. Author summaryIn animals, the earliest stages of embryogenesis are initially driven by proteins and RNAs that the mother provides via the egg; later development is controlled by the embryos own genes. The switch from maternal to zygotic control is called the maternal-zygotic transition (MZT). This conserved process involves degradation of maternal mRNAs, activation of zygotic genes, cell cycle lengthening, and morphological remodeling. All these events require precise control, but how they are coordinated remains incompletely understood. Here we show that the levels of a specific histone, H2A.Z, provide a timer for the MZT. In Drosophila, H2A.Z levels - both in the embryo overall and in nuclei - increase during the MZT. When we ectopically increased H2A.Z levels, specific MZT events occurred prematurely. Reducing H2A.Z levels had the opposite effect. Using mutant flies in which H2A.Z levels are ectopically increased in the nucleus but reduced in the embryo as a whole, we uncovered both nuclear and non-nuclear roles for H2A.Z in the establishment of developmental timing. Moreover, we observed similar outcomes in genetically manipulated zebrafish embryos. Our results are consistent with an ancient mechanism in which H2A.Z abundance functions as a timer of early embryogenesis.

developmental biology↗

bioRxiv2026

PanVariants: Best Practice for Pangenome-based Variant Calling Pipeline and Framework

BackgroundAlthough pangenome references offer richer population diversity compared to linear references, current mainstream pangenome-based variant callers are limited to detecting only known variants stored in the graph. To address this limitation, we developed PanVariants, a novel pipeline designed to improve the detection of both known and novel variants accurately. We systematically evaluated its performance against the traditional linear alignment solution (BWA+GATK/Manta) and the existing pangenome-aware solution (DRAGEN/PanGenie) in three contexts: small variants (SNVs/indels) and structural variants (SVs) accuracy in Genome in a Bottle samples, clinical detection on positive samples, and application in cohort-based joint calling. ResultsBy integrating k-mer-based and mapping-based methods, PanVariants significantly reduced variant errors (FPs + FNs), achieving a 73% reduction compared to BWA+GATK and a 45% reduction compared to DRAGEN for SNVs. Retraining the DeepVariant model with high-quality DNBSEQ data further decreased errors by 15%. For SVs detection, PanVariants attained an F1-score of 89.39%, markedly outperforming DRAGEN (68.18%) and BWA+Manta (58.33%), approaching long-read sequencing performance (95.22%). In validation using clinical positive samples, PanVariants successfully detected all expected pathogenic variants while PanGenie failed. In the cohort joint-calling analysis, PanVariants detected more variants, made fewer Mendelian inheritance errors, and gave better per-sample accuracy than GATK. ConclusionsPanVariants establishes a robust framework and best-practice pipeline for pangenome-based variant detection, achieving both sensitive novel variant discovery and high accuracy for SNVs, indels and SVs. Our systematic evaluation of optional processing steps and input variables offers practical guidance for users. Validated across diagnostic and population-based applications, our findings strongly support the transition from linear to pangenome references in future genomics.

bioinformatics↗