Biology subjects

Liang, C.

Publications and source records attributed to Liang, C..

At least 37 records · Page 2Linked to original sources

bioRxiv2026

Wetness modulates the effects of grazing on net ecosystem productivity in global grasslands

Overgrazing has induced widespread grassland degradation globally. However, how grazing intensity affects ecosystem carbon dioxide (CO2) fluxes with wetness fluctuations in grasslands at a global scale remains poorly understood. Here we measured ecosystem CO2 fluxes covering the 7th to 11th years of a continuous grazing experiment in a typical steppe, and conducted a meta-analysis of 585 observations by collecting relevant data in global grasslands. Our experimental results showed that mean gross primary productivity (GPP) and ecosystem respiration (ER) were decreased under heavy grazing (HG) compared with control without grazing (CK), whereas net ecosystem productivity (NEP) was not different between HG and CK in the typical steppe. The NEP was higher under light grazing in the wetter years, but it was not different between LG and CK under drier years in the typical steppe. The structural equation model showed that grazing altered NEP by increasing soil temperature and relative growth rate, while decreasing AGB. In contrast, grazing decreased GPP, ER and NEP, respectively, in global grasslands. Both our field experiment and the meta-analysis revealed that the response of NEP to light grazing, rather than heavy grazing, was lineally correlated with the wetness index. Higher wetness and aboveground biomass (AGB) increased the response of NEP to grazing in global grasslands. However, heavy grazing reduced NEP and AGB even under higher wetness indices in global grasslands, resulting from a loss of their resilience in long-term heavy grazing. These findings indicate that light grazing appears to be a promising management to promote plant relative growth rate and carbon sequestration. Overall, the meta-analysis and field experiment jointly provide global perspectives on the response of ecosystem CO2 fluxes to grazing intensity and improve our understanding of the factors influencing the response of ecosystem CO2 fluxes to grazing intensity.

ecology↗

bioRxiv2026

Measurement of tau protein and Aβ amyloid plaques in postmortem human brains of Down syndrome and Alzheimers disease by using IBETA autoradiography

The accumulation of tau tangles and A{beta} plaques are prominent neuropathologies that characterize Alzheimers disease (AD) and Down Syndrome (DS). Continuous developments of PET tracers as biomarkers can be supported by autoradiography to validate effectiveness and accuracy of binding properties that elucidate the pathophysiology of DSAD and AD. This in vitro comparative study evaluates [125I]IPPI binding to tau and [125I]IBETA binding to A{beta} plaques in the frontal cortex (FCX) and temporal cortex (TCX) of postmortem human brain slices of AD (n=5), DSAD (n=5), and cognitively normal (CN) (n=5) cases. With anti-tau and anti-A{beta} immunostains confirming the presence of tau and A{beta} plaques, [125I]IPPI and [125I]IBETA binding in autoradiographic images were significantly higher in DSAD and AD gray matter (GM) compared to CN. When comparing DSAD with AD, FCX and TCX GM binding was similar throughout DSAD and AD except in FCX GM where there was 48% more [125I]IPPI binding in DSAD than AD. In vitro drug inhibition studies revealed that [125I]IPPI binding was significantly inhibited with increasing harmine concentrations (IC50=115{+/-}40 nM) in DSAD FCX and TCX but KuFal194 minimally inhibited [125I]IPPI binding in the same cases. The GM/white matter ratios for DSAD ([125I]IPPI=4.1, [125I]IBETA=2.9) and AD ([125I]IPPI=4.2, [125I]IBETA=2.6) were significantly greater than CN ([125I]IPPI=1.3, [125I]IBETA=1.2). A positive correlation between [125I]IPPI and [125I]IBETA binding suggests a synergistic relationship between tau and A{beta} plaque in DSAD and AD pathology. This study demonstrates that [125I]IPPI and [125I]IBETA may serve as novel radiotracers in both DSAD and AD to continue diagnostic investigations in vivo.

neuroscience↗

bioRxiv2025

Flu Virus Infection in Juvenile Mice Leads to Lifelong Multi-Organ Damage and Parkinsonian Pathological Changes in Aging

The widespread prevalence of Long COVID underscores the potential for viral infections to exert prolonged effects on hosts long after initial recovery. Despite this recognition, the long-term and even lifelong consequences of viral infections remain poorly understood. In this study, we infected juvenile mice with influenza viruses and systematically examined the lifelong effects (from 4 to 450 days post-infection) of these infections. Pathological analysis revealed persistent lifelong damage in multiple organs, including chronic lung inflammation and fibrosis, along with significant cardiac and renal pathology. Viral infection led to substantial neuronal loss in key brain regions of mice (hippocampal CA1, CA3, and striatum) during middle and old age. Strikingly, we identified two hallmark pathological features of Parkinsons disease - dopaminergic neuron degeneration and Lewy body-like -synuclein inclusions - in middle and aged infected mice. Transcriptomic profiling demonstrated sustained upregulation of inflammation-related genes in both lung and blood tissues, correlating with observed pathological changes. Lung-derived secreted proteins, encoded by differentially expressed genes, may mediate cross-organ communication affecting cardiac, renal, and neurological function. Brain transcriptome analysis at three months post-infection revealed downregulation of neurodevelopmental genes, potentially contributing to subsequent neuronal loss and Parkinsonian pathology. These findings collectively suggest that pulmonary influenza infection can induce systemic multi-organ effects through both secretory pathways and chronic inflammatory responses. The study offers crucial insights for developing more effective strategies to prevent and manage infectious diseases and their long-term sequelae.

microbiology↗

bioRxiv2025

A K27-linked Ubiquitin Checkpoint Controls NOTCH Homeostasis

Cell surface receptors such as NOTCH1 must be tightly regulated to ensure developmental fidelity and prevent pathological activation. Although the proteolytic steps culminating in nuclear NOTCH1 signaling are established, how cells prevent excessive or uncontrolled activation has remained unresolved. Here we identify the autophagy-related protein UVRAG as a negative regulator of NOTCH1. Upon receptor activation, UVRAG, acting independently of autophagy, recruits and activates the E3-ligase ITCH to catalyze K27-linked ubiquitination of membrane-tethered NOTCH1, thereby licensing ESCRT-dependent lysosomal degradation. Disruption of the UVRAG-ITCH-ESCRT axis stabilizes activated NOTCH1 intermediates and amplifies oncogenic signaling. In T-cell leukemia models driven by constitutive NOTCH1 activity, restoring UVRAG expression reinstates receptor turnover, suppresses disease progression, and improves therapeutic response. These findings define a ubiquitin-directed safeguard circuit that enforces NOTCH1 signaling homeostasis and reveals a tunable axis for intervention in NOTCH1-driven cancers.

molecular biology↗

bioRxiv2025

scMOBA: A conversational single-cell Multi-Omics Brain Agent across species

Single-cell and spatial multi-omics are revolutionizing our understanding of the complexity in the developmental, aging, and diseased brain, but integrating this knowledge across modalities and species remains challenging. To bridge this gap, we propose scMOBA, a conversational single-cell Multi-Omics Brain Agent established by a large language model, a gene encoder, and a cross-attention projector. The scMOBA was pre-trained on 130 million single-cell and spatial multi-omics data spanning the entire brain across diverse species, development, aging and diseases. The pre-training utilized a novel multi-omics Feature-Question-Answer (FQA) paradigm, enabling the model to generate biological answers from feature inputs and textual queries. This unique scheme facilitates superior zero-shot inference capabilities without requiring additional fine-tuning. We demonstrate that scMOBA achieves state-of-the-art performance in fine-grained cell type classification across different species and modalities, as well as in batch correction and multi-omics data integration. Furthermore, scMOBA significantly boosts the accuracy of kinds of critical downstream tasks, including cell-type specific aging clock construction and disease status prediction. Overall, scMOBA serves as a powerful scientific discovery engine for multi-omics brain research, advancing the precision prediction and early intervention of neurological aging and diseases.

bioinformatics↗

bioRxiv2025

Scalable integration and prediction of unpaired single-cell and spatial multi-omics via regularized disentanglement

Deciphering cellular states requires methods capable of integrating large-scale heterogeneous single-cell and spatial omics data. However, these data are typically unpaired due to destructive assays and further confounded by modality heterogeneity, technical noise, and immense scale. Here we present scMRDR, a scalable computational framework based on regularized disentangled representation learning for integrating fully unpaired single-cell and spatial multi-omics datasets. Built on a unified and structure-preserving architecture, scMRDR removes the need for pairing supervision while maintaining computational efficiency, enabling scaling to large datasets spanning multiple disparate omics modalities. Across diverse real-world benchmarks, scMRDR demonstrates strong performance in batch correction, modality alignment, and biological signal preservation. The framework further supports cross-modal translation across omics modalities and enables spatial coordinate imputation for non-spatial single-cell datasets using a reference atlas. The resulting spatial mapping allows spatially resolved analyses, including identification of spatially variable genes and characterization of epigenetic regulatory programs in their native tissue context. These capabilities position scMRDR as a scalable and versatile framework for large-scale multi-omics integration.

genomics↗

bioRxiv2025

Adipose tissue cell states linked to progression and clinical subtypes of MASLD in human obesity

Adipose tissue dysfunction is a key determinant of inter-individual variability in obesity-associated comorbidities, yet the underlying tissue-level mechanisms linking adipose remodeling to progression of metabolic dysfunction-associated steatotic liver disease (MASLD) remain poorly defined. We applied single-nucleus RNA sequencing to abdominal subcutaneous adipose tissue (SAT) from individuals with severe obesity, stratified by histologically defined MASLD stage, and integrated these data with bulk RNA-seq from [~]200 individuals. MASLD was associated with adipocyte hypertrophy and near-depletion of an ADH1BHI adipocyte subset linked to improved lipid buffering and systemic metabolic health. Conversely, lipid-associated macrophages (LAMs) expanded in MASLD, coordinating lipid-handling and inflammatory programs in the myeloid compartment. In advanced metabolic dysfunction-associated steatohepatitis (MASH), we identified a senescence-associated PLAUHI progenitor subpopulation with pro-inflammatory signaling potential. Whereas LAMs were broadly enriched in MASLD subtypes, PLAUHI progenitors specifically marked a cardiometabolic MASLD endotype, characterized by type 2 diabetes and cardiovascular disease. These findings highlight cellular remodeling of adipose tissue as a potential driver of MASLD heterogeneity and progression.

cell biology↗

bioRxiv2025

Oral L-arginine cures arginase 1-dependent chronic cutaneous leishmaniasis by redirecting the T helper cell response

Leishmania (L.) mexicana-induced cutaneous leishmaniasis (CL) is a neglected tropical disease characterized by localized chronic ulcers (LCL) and, in rare cases, by disseminated skin lesions (DCL). The therapeutic options for CL are currently limited, and the immune dysregulation leading to chronicity of disease is poorly understood. Here, we identified interleukin (IL)-10-dependent upregulation of arginase 1 (ARG1) in cutaneous CX3CR1+ myeloid cells as central immunometabolic determinant of chronic CL in L. mexicana-infected C57BL/6 wild-type (WT) mice. Deletion of Arg1 in myeloid cells (Arg1{Delta}Cx3cr1) enabled parasite control and clinical healing. Single-cell RNA sequencing revealed that ARG1, together with interferon-{gamma} produced by T-helper 1 (Th1) cells, caused pathologic differentiation of Ly6Chigh monocytes into inflammatory macrophages (iMACs) that simultaneously expressed ARG1, nitric oxide synthase type 2 (NOS2) and the chemokines CXCL9/10. These Arg1+Nos2+Cxcl9/10+iMACs induced a lasting depletion of L-arginine in the skin, served as parasite niche, and maintained a self-perpetuating cycle of host cell recruitment. In Arg1{Delta}Cx3cr1 mice, the ARG1+NOS2+ host cell niche for the parasite was diminished. Prophylactic or therapeutic oral L-arginine supplementation restored tissue arginine levels, reduced parasite burden, and prevented or resolved chronic disease. L-arginine-treated mice showed enhanced T cell expansion and Th1 differentiation, remained free of clinical relapses, and were resistant to reinfection. As skin lesion biopsies from L. mexicana-infected LCL and DCL patients demonstrated a similar pattern of Th1/Th2 cytokine, Arg1 and Nos2 mRNA expression as seen in mice, we suggest metabolic reprogramming by oral L-arginine as a promising and easy-to-apply host-directed therapy for human L. mexicana CL. ONE SENTENCE SUMMARYArginase 1-mediated arginine depletion accounts for chronic cutaneous leishmaniasis, which can be prevented and even cured by oral L-arginine therapy.

immunology↗

bioRxiv2025

Gliomas phenocopy an inborn error of metabolism to drive neuronal activity and tumor growth

The metabolic hallmarks of high-grade glioma (HGG) are not fully understood. Human brain tissue metabolomics revealed that the creatine synthesis pathway intermediate guanidinoacetate (GAA) accumulated [~]100-fold in HGGs relative to controls, which was caused by imbalanced activities of enzymes in this pathway. Glioma cells secreted GAA rather than using it to produce creatine, implicating an unexpected function. GAA accumulates in GAMT deficiency, an inborn error of metabolism, and elevates neuronal excitability. Neuronal excitability is also increased in glioma and drives tumor growth through neuron-glioma interactions. We hypothesized that glioma-generated GAA excites surrounding neurons. Indeed, GAA induced neuronal hyperactivity by activating GABAA receptors and causing depolarizing GABA currents in glioma-associated neurons with dysregulated chloride homeostasis. Depleting tumoral GAA decreased electrochemical activity, neuron-glioma interactions, and tumor aggressiveness. Our findings unveil a new mechanism linking cancer metabolism with cancer neuroscience and leverage human genetics to nominate GAA synthesis as a target in gliomas.

cancer biology↗

bioRxiv2025

The gut microbiota directs vitamin A flux to regulate intestinal T cell development

The intestinal microbiota shapes adaptive immunity, but the mechanisms remain incompletely defined. Here, we show that the microbiota initiates the movement of retinoids--dietary vitamin A derivatives including retinol and retinoic acid--through a sequential pathway from epithelial cells to myeloid cells and ultimately to T cells in the mesenteric lymph nodes (mLNs). This cellular axis is traversed over three days. Microbe-associated molecular patterns (MAMPs) initiate retinoid flux by inducing expression of serum amyloid A (SAA) proteins. These epithelial retinol-binding proteins are necessary and sufficient for epithelial-to-myeloid cell retinoid transfer and for myeloid cell migration to the mLNs. In the mLNs, microbial antigen drives retinoid transfer from myeloid cells to developing T cells, culminating in T cell retinoid uptake and transcriptional programming. This pathway is activated during postnatal development, when gut adaptive immunity is first established. These findings reveal that the microbiota programs intestinal adaptive immunity by regulating immune cell access to a nutrient-derived developmental signal. HighlightsO_LIThe gut microbiota enables vitamin A flux to developing intestinal CD4 T cells. C_LIO_LIMicrobiota-induced SAA initiates vitamin A flux along a gut myeloid-T cell axis. C_LIO_LIMicrobial molecular patterns and antigen drive distinct steps of vitamin A flux. C_LIO_LIMicrobiota-driven vitamin A flux programs intestinal T cell homing and maturation. C_LI Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=192 HEIGHT=200 SRC="FIGDIR/small/674524v1_ufig1.gif" ALT="Figure 1"> View larger version (53K): org.highwire.dtl.DTLVardef@13b3906org.highwire.dtl.DTLVardef@11ceee3org.highwire.dtl.DTLVardef@87913forg.highwire.dtl.DTLVardef@50c9a0_HPS_FORMAT_FIGEXP M_FIG C_FIG

immunology↗

bioRxiv2025

Development of LYTACs via incorporating a nucleolin-targeting and lysosome-directed aptamer

Lysosomal targeting chimeras (LYTACs) represent an emerging class of bifunctional molecules that bridge extracellular target proteins with intrinsic lysosome-targeting receptors (LTRs) on the cell surface, facilitating endocytic internalization and subsequent lysosomal degradation of the targets. However, the therapeutic potential of LYTACs has been limited by the scarcity of suitable intrinsic LTRs. We previously identified an aptamer, SAPT8, that selectively targets nucleolin, a shuttling protein overexpressed on the surface of pathogenic FLSs in rheumatoid arthritis (RA), and induced its lysosomal degradation. In this study, we repurposed SAPT8 as a tumor-targeting and lysosome-directed ligand, leveraging the elevated expression of NCL on tumor cell surfaces. By conjugating SAPT8 with either the c-Met-binding aptamer SL1 or the small molecule inhibitor Tepotinib, we engineered novel LYTACs that demonstrated potent tumor-targeting capability and induced concurrent degradation of both c-Met and NCL, leading to significant antitumor effects. Furthermore, fusion of SAPT8 with VEGFR-2-targeting aptamer Apt02 generated LYTACs that simultaneously degraded VEGFR-2 and NCL, effectively suppressing RA-FLS activity. These results establish SAPT8 as a versatile platform for developing next-generation LYTACs, overcoming current limitations in extracellular protein degradation by circumventing dependence on endogenous LTRs. Graphic Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=69 SRC="FIGDIR/small/672993v1_ufig1.gif" ALT="Figure 1"> View larger version (35K): org.highwire.dtl.DTLVardef@975b74org.highwire.dtl.DTLVardef@f55565org.highwire.dtl.DTLVardef@b9639corg.highwire.dtl.DTLVardef@13aaba7_HPS_FORMAT_FIGEXP M_FIG C_FIG

pathology↗

bioRxiv2025

Mechanosensitive channel PIEZO1 enhances endometrial decidualization via BECN1-dependent autophagy

The mechanosensitive ion channel PIEZO1 plays critical roles in physiological and pathological processes in response to various types of mechanical forces, including shear stress, stretch, and extracellular matrix (ECM) stiffness. Decidualization is crucial for a successful pregnancy, characterized by the differentiation of fibroblastic endometrial stromal cells into round, secretory decidual cells, along with the rapid remodeling of the ECM. Herein, we report that PIEZO1 plays a crucial role in enhancing decidualization in response to extracellular matrix (ECM) stiffness and cell contraction. Uterine-specific knockout of Piezo1 using Pgr-Cre in mice results in subfertility due to decidualization impairment in mid-late pregnancy. Silencing of PIEZO1 in human endometrial stromal cells also results in impaired decidualization. Treatment with the PIEZO1 agonist Yoda1 enhances decidualization in both in vivo and in vitro models. Stromal cells growing on ECM with 25 kPa stiffness display a better decidualization response than cells seeded on softer 2 kPa surface or harder surface of the regulator petri dish, and this difference is abolished by null of Piezo1. Consistent with PIEZO1 as a Ca2+ modulator, blocking of intracellular Ca2+ or pCaMKII significantly inhibits Yoda1-enhanced decidualization. Further investigation reveals that BECN1-dependent autophagy acts as the downstream of PIEZO1. Silencing of Beclin1 abolishes Yoda1-induced decidualization, while Tat-BECN1 fully rescues impaired decidualization caused by the lack of PIEZO1. Finally, the lower expression of PIEZO1 is associated with impaired decidualization in the endometrium of endometriotic baboons. In conclusion, we have uncovered a novel mechanism of decidualization that is regulated by PIEZO1-mediated mechanotransduction, providing further insight into decidualization studies. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=187 HEIGHT=200 SRC="FIGDIR/small/668790v1_ufig1.gif" ALT="Figure 1"> View larger version (68K): org.highwire.dtl.DTLVardef@2d25faorg.highwire.dtl.DTLVardef@186e56org.highwire.dtl.DTLVardef@1f3f61borg.highwire.dtl.DTLVardef@1a26bb7_HPS_FORMAT_FIGEXP M_FIG C_FIG

physiology↗

bioRxiv2025

Targeting nucleolin facilitates the development of blood-tumor barrier-penetrating and glioblastoma-specific PROTACs

Targeted therapy for glioblastoma (GBM) is challenged by the blood-tumor barrier (BTB). Extracellular vesicles (EVs) from GBM cells play a role in transforming BBB into BTB, although the mechanisms are not fully understood. This study identifies nucleolin (NCL), a nucleomembrane shuttling protein, as being transferred from GBM cells to the surface of brain capillary endothelial cells, facilitating BTB formation. The aptamer AS1411, which targets NCL, is shown to cross the BTB via receptor-mediated transcytosis (RMT) and selectively recognize GBM cells in an NCL-dependent manner. Beyond its targeting capabilities, AS1411 has been repurposed to recruit the E3 ligase MDM2 in PROTACs, leveraging the intracellular interaction of NCL with MDM2. Utilizing AS1411s multifunctionality in BTB penetration, GBM cell targeting, and MDM2 recruitment, we conjugated AS1411 to VEGFR2 or EGFR ligands to create PROTAC degraders. These constructs induce NCL- and MDM2-dependent ubiquitination and degradation of VEGFR2 or EGFR, demonstrating significant anti-GBM efficacy both in vitro and in vivo, with no toxicity to normal cells. Overall, NCL from GBM-derived EVs emerges as a crucial mediator of BTB formation and serves as a receptor for AS1411-mediated RMT, paving the way for developing PROTACs that effectively traverse BTB and target GBM. GRAPHICAL ABSTRACTS O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=139 SRC="FIGDIR/small/666084v1_ufig1.gif" ALT="Figure 1"> View larger version (43K): org.highwire.dtl.DTLVardef@79778org.highwire.dtl.DTLVardef@6984d8org.highwire.dtl.DTLVardef@1909eddorg.highwire.dtl.DTLVardef@1adf342_HPS_FORMAT_FIGEXP M_FIG C_FIG

cancer biology↗

bioRxiv2025

A Thiopurine-like Mutagenic Process Defines TGCT Subtypes

Testicular germ cell tumors (TGCTs) are the most common malignancy in young men, exhibit a unique developmental origin and exceptional chemosensitivity. However, the molecular distinctions between TGCT subtypes remain poorly understood. Here we present a comprehensive genomic analysis of 252 treatment-naive primary TGCTs, integrating deep whole-genome sequencing with matched transcriptomic and epigenomic data. We identify new driver genes and uncover defining features of TGCTs, including pervasive chromosome X amplification with subtype-specific X chromosome inactivation, and a germ cell-like transcriptional program. Although previously reported, whole genome doubling (WGD) in TGCTs is further characterized here as ubiquitous, developmentally early, and associated with age at onset. Seminomas are enriched for early driver mutations, secondary WGD events, sustained XIST expression and replication stress-associated indel mutational signatures, while non-seminomas show greater structural complexity, subclonal diversity, relatively earlier-onset WGD, extended tumor latency, and telomere elongation. Moreover, we identify a mutational signature, SBS87, that is exceptionally rare across cancers with exception of thiopurine-treated leukemia, but strikingly prevalent in TGCT, especially non-seminomas. SBS87 is linked to extended tumor latency and telomere elongation, implicating possible environmental or endogenous processes that mimic thiopurine-induced DNA damage in TGCT pathogenesis. Collectively, our findings define TGCTs as molecularly distinct tumors shaped by early genomic instability and highlight SBS87 as a novel mutational footprint with potential etiologic and clinical relevance.

genomics↗

bioRxiv2025

Nonequivalence of Zfp423 premature termination codons in mice.

Genetic variants that introduce a premature termination codon (PTC) are often assumed equivalent and functionally null. Exceptions depend on the specific architectures of the affected mRNA and protein. Here we address phenotypic differences among early truncating variants of mouse Zfp423, whose phenotypes resemble Joubert Syndrome and Related Disorders (JSRD). We replicate quantitative differences previously seen between presumptive null PTC variants based on their position in the coding sequence. We show with reciprocal congenic strains that large phenotype differences between two PTC variants with the same predicted stop and reinitiation codons is due to the specific allele rather than different strain backgrounds, with no evidence for induced exon skipping. Differences in RNA structure, however, could influence translation rate across the affected exon. Using a reporter assay, we find differences in translational reinitiation between two deletion variants that corelate with predicted RNA structure rather than distance from the canonical initiation codon. These results confirm and extend earlier evidence for differences among Zfp423 PTC variants, identify parameters for translational reinitiation after an early termination codon, and reinforce caution in the null interpretation of early PTC variants.

genetics↗

bioRxiv2025

Cross-Species Prediction of Histone Modifications in Plants via Deep Learning

The regulation of gene expression in plants is governed by complex interactions between cis-regulatory elements and epigenetic modifications such as histone marks. While deep learning models have achieved success in predicting regulatory features from DNA sequence, their cross-species generalizability in plants remains largely unexplored. In this study, we systematically evaluated the ability of deep learning models to predict histone modifications across plant species using a multi-stage framework based on the Sei architecture. We trained species-specific models for Arabidopsis (A. thaliana), rice (O. sativa), and maize (Z. mays), achieving high within-species predictive performance (AUROC > 0.94) and strong agreement between predictions and experimental ChIP-seq profiles. However, cross-species predictions showed reduced performance with increasing phylogenetic distance, highlighting limited model transferability between monocots and dicots. To improve generalization, we built family-level models by training on multiple species across the Poaceae and Brassicaceae families. These models demonstrated robust predictive power in completely unprofiled species--those entirely unused in training set--highlighting the models adaptability to novel plant genomes based solely on conserved regulatory syntax. In contrast, cross-family models produced inconsistent results, with reliable performance only in species sharing conserved regulatory features. Lastly, we developed an easy-to-use pipeline that predicts genome-wide chromatin signals directly from DNA sequences. Our findings demonstrate that phylogenetically informed model training significantly improves cross-species epigenomic prediction, offering a scalable computational strategy for functional annotation in non-model and agriculturally important plants.

bioinformatics↗

bioRxiv2025

Deciphering Biosynthetic Gene Clusters with a Context-aware Protein Language Model

Microbial secondary metabolites, synthesized by biosynthetic gene clusters (BGCs), offer vast potential for biotechnological applications. Among BGC profiling techniques, computational detection methods face challenges, including time-consuming alignment and reliance on predefined profiles. To address these, we present BGC-Finder, an end-to-end pipeline utilizing protein language models for BGC detection and annotation from microbial genomes and metagenomes. This approach achieves remarkable increase in profiling speed of up to 100-fold, and employs genomic context-aware modeling to facilitate interpretable genetic essentiality assessment and large-scale BGC clustering. BGC-Finder outperformed traditional methods, successfully detecting 9.49% more biosynthetic-core genes and 27.70% more cytochrome P450s in 742 experimentally-validated BGCs. Notably, it retrieved 31 remote biosynthetic homologs from 210 polar marine metagenomes and identified 4,585 BGCs with 6,388 core genes from 256 fungal genomes. These findings highlight BGC-Finders capability to illuminate "microbial biosynthesis dark matter" (sequence-unrelated, function-similar biosynthetic enzymes) and expedite natural product discovery. HighlightsO_LIBGC-Finder is an accurate and ultrafast pipeline leveraging protein language models (pLMs) to predict and annotate biosynthetic gene clusters (BGCs) from microbial genomes and metagenomes. C_LIO_LIThe genomic context-aware model enables interpretable analysis: attention-driven identification of essential biosynthetic genes and embedding-guided BGC clustering. C_LIO_LIBGC-Finder sensitively retrieves remote homologous BGCs from both bacteria and fungi genomes, uncovering hidden microbial biosynthesis dark matter. C_LIO_LIWe discovered a non-ribosomal peptide synthetase (NRPS) family, which involved into function-specific BGCs in two evolutionarily distant fungi. C_LI

bioinformatics↗

bioRxiv2025

Tulp3 quantitative alleles titrate requirements for viability, brain development, and kidney homeostasis but do not suppress Zfp423 mutations in mice.

Tubby-like protein 3 (TULP3) regulates receptor trafficking in primary cilia and antagonizes SHH signaling. Tulp3 knockout mice are embryonic lethal with developmental abnormalities in multiple organs, while tissue-specific knockouts and viable missense alleles cause polycystic kidney disease. Human patients with TULP3 mutations present with variable, but often multi-organ fibrotic disease. We previously showed that mouse and human Tulp3 expression is negatively regulated by ZNF423, which is required for SHH sensitivity in some progenitor cell models. The level of TULP3 function required to prevent mutant phenotypes has not been known. Here we report a Tulp3 quantitative allelic series, designed by targeting the polypyrimidine tract 5 to the splice acceptor of a critical exon, that shows distinct dose-response effects on viability, brain overgrowth, weight gain, and cystic kidney disease. We find limited evidence for genetic interaction with Zfp423 null or hypomorphic mutations. Together, these results establish an approach to developing quantitative allelic series by exon exclusion, rank-order dose-sensitivity of Tulp3 phenotypes, and model thresholds for TULP3 function to prevent severe outcomes. Author SummaryTULP3 protein plays critical roles in regulating receptor trafficking and signaling in the primary cilium. Mutations in the TULP3 gene can cause severe, multi-organ disorders in both mice and humans, yet the amount of TULP3 activity needed to avoid these outcomes has been unclear. In this study, we used precise genome editing in mice to create a set of new Tulp3 gene variants that reduce TULP3 expression to varying degrees. This allowed us to test how much TULP3 is required for survival, normal brain and kidney development, and weight regulation. We found that as little as 5% of normal TULP3 levels is enough to avoid lethal birth defects, but still leads to obesity, mild brain overgrowth, and progressive kidney cysts preceded by reductions in cilium frequency and length in situ. The severity of these effects was related to TULP3 protein levels, highlighting a dose-dependent response. We also investigated whether reducing TULP3 levels would suppress brain abnormalities in Zfp423 mutant mice, based on prior evidence of a genetic interaction, but did not find evidence to support this effect. Our work provides a framework for understanding how varying levels of TULP3 affect various organ systems and offers a general strategy for creating quantitative genetic models of human disease.

genetics↗