Biology subjects

Yang, J.

Publications and source records attributed to Yang, J..

At least 325 records · Page 18Linked to original sources

bioRxiv2025

A SNP Foundation Model: Application in Whole-Genome Haplotype Phasing and Genotype Imputation

Millions of human genomes have been genotyped by national biobanks worldwide. Training large language models (LLM) with this data may lead to a universal model of human genome with tremendous potential. Yet the quadrillions (1015) of nucleotides-- resulting from genome length multiplied by population size--pose formidable challenges for modeling. In this study, we propose a novel AI framework designed to scale with this data and support diverse analytical tasks. To demonstrate this scheme, we developed SNPBag--a foundation model focusing on single nucleotide polymorphism (SNP). With 0.8 billion parameters, it is trained on one million synthesized human genomes, corresponding to a total of 6 trillion SNP tokens. SNPBag showed superior performance in benchmarking of multiple tasks. In genotype imputation, it achieves state-of-the-art (SOTA) accuracy. In haplotype phasing, it rivals the best method with a 72-fold speedup. By encoding 6 million SNPs per genome into a 0.75 MB embedding, SNPBag enables efficient storage, transfer and downstream applications. In particular, the genome embeddings facilitate rapid ancestry inference across global populations and detection of genetic relationships up to 12th-degree relatives. Collectively, SNPBag introduces a new paradigm for scalable, unified and multitask analysis of the ever-growing human variation data.

genomics↗

bioRxiv2025

Sources of non-uniform coverage in short-read RNA-Seq data

The origin of several normal cellular functions and related abnormalities can be traced back to RNA splicing. As such, RNA splicing is currently the focus of a vast array of studies. To quantify the transcriptome, short-read RNA-Seq remains the standard assay. The primary technical artifact of RNA-Seq library prep, which severely interferes with analysis, is extreme non-uniformity in coverage across transcripts. This non-uniformity is present in both bulk and single-cell RNA-Seq and is observed even when the sample contains only full-length transcripts. This issue dramatically affects the accuracy of isoform-level quantification of multi-isoform genes. Understanding the sources of this non-uniformity is critical to developing improved protocols and analysis methods. Here, we explore eight potential sources of non-uniformity. We demonstrate that it cannot be explained by one factor alone. We performed targeted experiments to investigate the effect of fragment length, PCR ramp rate, and ribosomal depletion. We assessed existing data sets with varying sample quality, PCR cycle number, reverse transcriptase, and technical or biological replicates. We found evidence that interference of reverse transcription by secondary structure is unlikely to be the major contributing factor, that rRNA pull-down methods do not cause non-uniformity, that PCR ramp rate does not substantially impact non-uniformity, and that shorter fragments do not reduce non-uniformity. All these findings contradict prior publications or recommendations.

bioinformatics↗

bioRxiv2025

Microglial plasticity governed by state-specific enhancer landscapes

Single-cell transcriptomic studies have identified distinct microglial subpopulations with shared and divergent gene signatures across development, aging and disease. Whether these microglial subsets represent ontogenically separate lineages of cells, or they are manifestations of plastic changes of microglial states downstream of some converging signals is unknown. Furthermore, despite the well-established role of enhancer landscapes underlying the identity of microglia, to what extent histone modifications and DNA methylation regulate microglial state switches at enhancers have not been defined. Here, using genetic fate mapping, we demonstrate the common embryonic origin of proliferative-region-associated microglia (PAM) enriched in developing white matter, and track their dynamic transitions into disease-associated microglia (DAM) and white matter-associated microglia (WAM) states in disease and aging contexts, respectively. This study links spatiotemporally discrete microglial states through their transcriptomic and epigenomic plasticity, while revealing state-specific histone modification profiles that govern state switches in health and disease.

neuroscience↗

bioRxiv2025

Single-Cell Genomics Elucidates Molecular Variations and Regulatory Mechanisms in Circulating Immune Cells

The human peripheral blood displays diverse molecular characteristics across populations, understanding the drivers and underlying mechanisms of which remains challenging. Here, we introduce the Chinese Immune Multi-Omics Atlas (CIMA), elucidating sex-, age-, and genetic-related molecular variations by analyzing multi-omics data from 428 adults with over 10 million immune cells. CIMA generated an enhancer-driven gene regulatory network, identifying 237 high-quality regulons and revealing cell type-specific regulatory mechanisms. Additionally, 11,521 lead cis-expression quantitative trait loci (eQTLs) and 46,339 chromatin accessibility QTLs (caQTLs) were identified at cell type level. CIMA also uncovered pleiotropic associations among immune-related disease risk loci, eQTLs, and caQTLs in a cell type-specific manner. Lastly, a novel cell language model, CIMA-CLM, was developed to predict chromatin accessibility and noncoding variant effects using chromatin sequences and gene expressions. This work represents a population-scale multi-omics resource of human immune cells, providing a valuable reference for future investigation of immune-related diseases.

immunology↗

bioRxiv2025

Dietary protein source mediates colitis pathogenesis through bacterial modulation of bile acids

Introductory paragraphEvidence-based dietary recommendations for individuals with inflammatory bowel diseases (IBD) are limited. Red meat consumption is associated with increased IBD incidence and relapse in patients, suggesting that switching to a plant-based diet may limit gut inflammation. However, the mechanisms underlying the differential effects of these diets remain poorly understood. Feeding diets containing plant- or animal-derived proteins to murine colitis models revealed that mice given a beef protein (BP) diet exhibited the most severe colitis, while mice fed pea protein (PP) developed mild inflammation. The colitis-promoting effects of BP were microbially-mediated as determined by bacterial elimination or depletion and microbiota transplant studies. In the absence of colitis, BP-feeding reduced abundance of Lactobacillus johnsonii and Turicibacter sanguinis and expanded Akkermansia muciniphila, which localized to the mucus in association with decreased mucus thickness and quality. BP-fed mice had elevated primary and conjugated fecal bile acids (BAs), and taurocholic acid administration to PP-fed mice worsened colitis. Dietary psyllium protected against BP-mediated inflammation, restored BA-modulating commensals and normalized BA ratios. Collectively, these data suggest that the protein component of red meat may be responsible, in part, for the colitis-promoting effects of this food source and provide insight into dietary factors that may influence IBD severity.

microbiology↗

bioRxiv2025

fCUT&Tag-seq: An Optimized CUT&Tag-based Method for High-Resolution Histone Modification and Chromatin-Binding Protein Profiling in both Model and Plant Pathogenic Fungi

Histone modifications and chromatin-binding proteins play crucial roles in regulating gene expression in eukaryotes, with significant implications for fungal pathogenicity and development. However, profiling these modifications or proteins across the genome in fungi remains challenging due to the technical limitations of the traditional, widely used ChIP-Seq method. Here, we present an optimized CUT&Tag-Seq protocol (fCUT&Tag-Seq) specifically designed for filamentous fungi and dimorphic fungi. Our approach involves the preparation of protoplasts and nuclear extraction to enhance antibody accessibility, along with formaldehyde crosslinking to improve protein-DNA binding efficiency. We then successfully applied fCUT&Tag-Seq to accurately profile multiple histone modifications like H3K9me3, H3K27me3, H3K4me3, and H3K18ac, across different plant pathogenic or model fungal species, including Verticillium dahliae, Neurospora crassa, Fusarium graminearum, and Sporisorium scitamineum, showing good signal-to-noise ratios, reproducibility, and detection sensitivity. Furthermore, we extended this method to profile chromatin-binding proteins, such as the histone acetyltransferase Gcn5. This study establishes fCUT&Tag-Seq as a robust and useful tool for fungal epigenetic research, enabling detailed exploration of chromatin dynamics and advancing our understanding of fungal gene regulation, development, and pathogenicity. Impact StatementWe developed a faster, lowLJinput method to study how genes are turned on and off in fungi, even in tough species that are difficult to analyze with standard methods. Our new approach, named fCUT&Tag-Seq, requires only 10,000 cells and can be completed in just two days. It delivers clearer, more reliable results and has already been successfully applied to multiple fungi, including crop pathogens. By revealing the molecular "control switches" that govern fungal development and virulence, we expect it will accelerate basic research and help identify new targets for controlling destructive plant diseases.

microbiology↗

bioRxiv2025

Shallow-angle intracranial cannula for repeated infusion and in vivo imaging with multiphoton microscopy

Multiphoton microscopy serves as an essential tool for high-resolution imaging of the living mouse brain. To facilitate optical access to the brain during imaging, the cranial window surgery is commonly used. However, this procedure restricts physical access above the imaging area and hinders the direct delivery of imaging agents and drugs. To overcome this limitation, we have developed a cannula delivery system that enables the implantation of a low-profile cannula nearly parallel to the brain surface at angles as shallow as 8 degrees, while maintaining compatibility with multiphoton microscopy. To validate this approach, we perform direct infusion and imaging of various fluorescent cell markers in the brain. Additionally, we successfully demonstrate tracking of degenerating neurons over time in Alzheimers disease mice using Fluoro-Jade C. Furthermore, we show longitudinal imaging of brain tissue partial pressure of oxygen using a phosphorescent oxygen sensor. Our developed technique should enable a wide range of new longitudinal imaging studies in the mouse brain.

neuroscience↗

bioRxiv2025

DNAHX: a novel, non-motile dynein heavy chain subfamily, identified by cryo-EM endogenously

Ciliogenesis and cilia motility rely on the coordinated actions of diverse dyneins, yet the complexity of these motor proteins in cilia has posed challenges for understanding their specific roles. Traditional evolutionary analyses often overlook key family members due to technical limitations. Here, we present a cryo-EM-based, bottom-up approach for large-scale, de novo protein identification and functional prediction of endogenous axonemal dynein complexes. This approach led to the identification of a novel dynein heavy chain subfamily (XP_041462850), designated as DNAHX, from sea urchin sperm. Phylogenetic analysis indicates that DNAHX branches from the outer-arm dynein alpha chain during evolution and is found in specific animal lineages with external fertilization. DNAHX contains multiple insertions throughout the protein, locking DNAHX permanently in a pre-powerstroke state. The AAA1 site exhibits poor conservation of essential ATPase motifs, consistent with DNAHXs non-motile nature. DNAHX also forms a heterodimeric dynein complex, which we named dynein-X, with another dynein heavy chain and accessory chains. Furthermore, a subset of dynein-X displays an autoinhibited phi particle conformation, potentially facilitating the intraflagellar transport of axonemal dyneins. Our discovery of the novel, non-motile dynein heavy chain and the dynein-X complex provides valuable insights into the evolution of dyneins and potentially their diverse cellular functions.

biophysics↗

bioRxiv2025

Genetically encoded mechano-sensors with versatile readouts and compact size

Mechanical forces are critical for virtually all fundamental biological processes, yet quantification of mechanical forces at the molecular scale in vivo remains challenging. Here, we present a new strategy using calibrated coiled coils as genetically encoded, compact, tunable, and modular mechano-sensors to substantially simplify force measurement in vivo, via diverse readouts (luminescence, fluorescence and analytical biochemistry) and instrumentation readily available in biology labs. We demonstrate the broad applicability and ease-of-use of these coiled coil mechano-sensors by measuring forces during cytokinesis (formin Cdc12) and endocytosis (epsin Ent1) in yeast, force distributions in nematode axons ({beta}-spectrin UNC-70), and forces transmitted to the nucleus (mini-nesprin-2G) and within focal adhesions (vinculin) in mammalian cells. We report discoveries in intracellular force transmission that have been elusive to existing tools.

cell biology↗

bioRxiv2025

Inhibition of Glutamine Metabolism Suppresses Tumor Progression through Remodeling of the Macrophage Immune Microenvironment

BackgroundTargeting glutamine metabolism has emerged as a promising strategy in cancer therapy. However, several barriers, such as in vivo anti-tumor efficacy, drug toxicity, and safety, remain to be overcome to achieve clinical utility. Prior preclinical in vivo studies had generated encouraging data showing promises of cancer metabolism targeting drugs, although most were performed on immune-deficient murine models. It is being recognized that aside from tumor cells, normal cells such as immune cells in the tumor microenvironment may also utilize glutamine for maintaining physiological functions. To provide an in-depth view of glutamine antagonist (GLNi) treatment on the tumor immune microenvironment, the current study made several unique approaches. MethodFirst, to evaluate GLNi treatment modality that potentially involves immune cells, the study was performed on immunocompetent murine models of gynecological cancers. Second, to enhance safety and reduce potential off-target effects, we developed a GLNi prodrug, JHU083, which is bio-activated restrictively in cancer tissues. Third, to unbiasedly decode the response of single cells in the tumor microenvironment to GLNi treatment, single-cell RNA sequencing (scRNA-seq) was performed on cells prepared from tumors of the JHU083 or vehicle control-treated mice. ResultsIn both immunocompetent murine tumor models, we observed a significant anti-tumor efficacy, resulting in reduced tumor burden and impeded tumor progression. Similarly, in both tumor models, scRNA-seq revealed significantly impeded immunosuppressive M2-like macrophages by JHU083, while the treatment spared pro-inflammatory M1-like tumor macrophages. In many tumor microenvironment (TME) cells, JHU083 downregulated genes regulated by Myc and hypoxia. M2 macrophages greater sensitivity to glutamine antagonism when compared to M1 macrophages or monocytes was further validated on ex vivo cultures of bone marrow-derived macrophages. ConclusionOur findings support a converged mechanism of glutamine metabolism antagonists. JHU083 exerted its anti-tumor efficacy through not only direct targeting of glutamine-addicted cancer cells but also by suppressing glutamine-dependent M2 macrophages, leading to a shift in the M1/M2 macrophage landscape in favor of an immune-stimulatory microenvironment.

cancer biology↗

bioRxiv2025

PRPS activity tunes redox homeostasis in Myc-driven lymphoma

Myc hyperactivation coordinately regulates numerous metabolic processes to drive lymphomagenesis. Here, we elucidate the temporal and functional relationships between the medley of pathways, factors, and mechanisms that cooperate to control redox homeostasis in Myc-overexpressing B cell lymphomas. We find that Myc overexpression rapidly stimulates the oxidative pentose phosphate pathway (oxPPP), nucleotide synthesis, and mitochondrial respiration, which collectively steers cellular equilibrium to a more oxidative state. We identify Myc-dependent hyperactivation of the phosphoribosyl pyrophosphate synthetase (PRPS) enzyme as a primary regulator of redox status in lymphoma cells. Mechanistically, we show that genetic inactivation of the PRPS2 isozyme, but not PRPS1, in MYC-driven lymphoma cells leads to elevated NADPH levels and reductive stress-mediated death. Employing a pharmacological screen, we demonstrate how targeting PRPS1 or PRPS2 elicits opposing sensitivity or resistance, respectively, to chemotherapeutic agents affecting the thioredoxin and glutathione network, thus providing a therapeutic blueprint for treating MYC-driven lymphomas.

cancer biology↗

bioRxiv2025

Polymerase mutations underlie adaptation of H5N1 influenza virus to dairy cattle and other mammals.

In early 2024, an unprecedented outbreak of H5N1 high pathogenicity avian influenza was detected in dairy cattle in the USA1. As of mid-2025 the epidemic is ongoing, resulting in spillbacks into poultry, wild birds and other mammals including humans2. Here, we present molecular and virological evidence that the cattle B3.13 genotype H5N1 viruses rapidly accumulated adaptations in polymerase genes that enabled better replication in bovine cells and tissues, as well as cells of other mammalian species including humans and pigs. We find evidence of several mammalian adaptations gained early in the evolution of these viruses in cattle including PB2 M631L, which is found in all cattle sequences, and PA K497R, which is found in the majority. Structurally, PB2 M631L maps to the polymerase-ANP32 interface, an essential host factor for viral genome replication. We show that this mutation adapts the polymerase to better interact with bovine ANP32 proteins, particularly ANP32A, and thereby enhances virus replication in bovine mammary systems and primary human airway cultures. Importantly, we show that ongoing evolution during 2024 and 2025 in the PB2 gene, including E627K and a convergently arising D740N substitution, further increase polymerase activity and virus replication in a range of mammalian cells. Thus, the continued circulation of H5N1 in dairy cattle not only allows virus adaption improving replicative ability in cattle, but also increases the risk of zoonotic spillover.

microbiology↗

bioRxiv2024

A nucleotide code governs Lis1's ability to relieve dynein autoinhibition

Dynein-1 is a microtubule motor responsible for the transport of cytoplasmic cargoes. Activation of motility requires it first overcome an autoinhibited state prior to its assembly with dynactin and a cargo adaptor. Studies suggest that Lis1 may relieve dyneins autoinhibited state. However, evidence for this mechanism is lacking. We first set out to determine the rules governing dynein-Lis1 binding, which reveals that their binding affinity is regulated by the nucleotide-bound states of each of three nucleotide-binding pockets within the dynein motor domain. We also find that distinct nucleotide codes coordinate dynein-Lis1 binding stoichiometry by impacting binding affinity at two different sites within the dynein motor domain. Electron microscopy reveals that a 1 Lis1:1 dynein complex directly promotes an open, uninhibited conformational state of dynein, whereas a 2:1 complex resembles the autoinhibited state. Cryo-EM analysis reveals the structural basis for Lis1 opening dynein relies on interactions with the linker domain.

biochemistry↗

bioRxiv2024

Nde1 Promotes Lis1 Binding to Full-Length Autoinhibited Human Dynein-1

Cytoplasmic dynein-1 (dynein) is the primary motor for the retrograde transport of intracellular cargoes along microtubules. The activation of the dynein transport machinery requires the opening of its autoinhibited Phi conformation by Lis1 and Nde1/Ndel1, but the underlying mechanism remains unclear. Using biochemical reconstitution and cryo-electron microscopy, we show that Nde1 significantly enhances Lis1 binding to autoinhibited dynein and facilitates the opening of Phi. We discover a key intermediate step in the dynein activation pathway where a single Lis1 dimer binds between the Phi-like (PhiL) motor rings of dynein. In this "PhiL-Lis1", Lis1 interacts with one of the motor domains through its canonical interaction sites at the AAA+ ring and stalk and binds to the newly identified AAA5, AAA6, and linker regions of the other motor domain. Mutagenesis and motility assays confirm the critical role of the PhiL-Lis1 interface. This intermediate state is instantly and efficiently formed in the presence of Nde1, but Nde1 is not part of the PhiL-Lis1. These findings provide key insights into the mechanism of how Nde1 promotes the Lis1-mediated opening of Phi dynein.

biophysics↗

bioRxiv2024

MethylQUEEN: A Methylation Encoded DNA Foundation Model

DNA 5-methylcytosine (5mC) modification plays a pivotal role in many biological processes, yet 5mC information and pattern hidden behind remains to be explored. Here, we develop Methylation Language Model based on Quintuple Bidirectional Transformer (MethylQUEEN), a novel pre-trained DNA methylation foundation model capable of sensing methylation states and covering the genome-wide methylation landscape. Through tailored methylation-prone pre-training, MethylQUEEN effectively captured epigenetics information hidden within the DNA sequences: it accurately traces DNAs tissue-of-origin, and successfully recovers the expression profile through methylation states. Integrative analysis on MethylQUEENs attention scores also enables us to reveal the unique methylation status of a tissue for precise disease detection, and identifying key regulatory 5mC sites for disease intervention. As a result, MethylQUEEN signifies a new paradigm in methylation analysis for various biological problems. Besides, our study demonstrates the effectiveness of directly integrating methylation information into pre-training, offering new perspectives and methodologies for a range of methylation-related biological processes. It serves as an initial exploration for the development of more comprehensive epigenomic models.

genomics↗

bioRxiv2024

TEAD promotes lineage progression of subpallial neural progenitor cells independent of YAP/TAZ

The TEAD family of transcription factors are best known as the DNA-binding factor in the Hippo pathway, where they act by interacting with transcriptional coactivators YAP and TAZ (YAP/TAZ). Despite the importance of the Hippo pathway, the in vivo functions of TEAD in mammals have not been well established. By comparing mouse mutants lacking TEAD1 and TEAD2 (TEAD1/2) to those lacking YAP/TAZ, we found that TEAD1/2 have both YAP/TAZ-dependent and -independent functions during ventral telencephalon development. TEAD1/2 loss and YAP/TAZ loss similarly disrupt neuroepithelial apical junctions. However, the impacts of their losses on progenitor lineage progression are essentially opposite: Whereas YAP/TAZ loss depletes early progenitors and increases later progenitors--consistent with their established function in promoting progenitor self-renewal and proliferation, TEAD1/2 loss expands early progenitors and reduces late progenitors, indicating that TEAD1/2 promote lineage progression. We further show that TEAD1/2 promote neural progenitor lineage progression by, at least in part, inhibiting Notch signaling and by cooperating with Insulinoma-associated 1 (INSM1). Orthologs of TEAD and INSM1 have been shown to cooperatively regulate neuronal cell fate decisions in worms and flies. Our study reveals a remarkable evolutionary conservation of the function of this transcription factor complex during metazoan neural development.

developmental biology↗

bioRxiv2024

Defective DcpS Decapping Manifests in Creatine Deficiency Syndrome and Neurological impairment

Biallelic mutations in the DCPS gene disrupting the decapping activity of the scavenger decapping protein DcpS, leads to neurodevelopmental deficiencies and intellectual disability. However, the molecular basis for the neurogenesis defects in these individuals remains unknown. Here we show that cells derived from individuals with a DCPS mutation harbor a creatine deficiency and a corresponding elevation of the creatine precursor, guanidinoacetate (GAA). The altered metabolite levels are a consequence of a reduction in both the mRNA and protein levels for the enzyme that converts GAA into creatine, guanidinoacetate methyltransferase. Importantly, the compromised neurogenesis and neurite outgrowth phenotypes observed during the differentiation of DcpS mutant patient derived induced pluripotent stem cell differentiation into neurons was reversed upon supplementation of creatine monohydrate. These findings suggest creatine deficiency as the major underlying factor for the neurogenetic defect detected in DcpS mutant cells and a potential driver of the neurological deficiencies in affected individuals.

cell biology↗

bioRxiv2024

Extracellular Exosomal RNAs are Glyco-Modified

Epitranscriptomic modifications play pivotal roles in regulating RNA function, encompassing base alterations and the addition of both canonical m7G and noncanonical nucleotide metabolite caps. Recently, the spectrum of modifications has extended to include glyco modification at the 5 cap or within the RNA. Despite this expansion, the functional implications of glyco modification on RNA remain elusive. Our study reveals that mammalian cells labeled with N-azidoacetylgalactosamine-tetraacylated (Ac4GalNAz) produce small noncoding and nonpolyadenylated glyco-modified RNA (glycoRNA), primarily localized within exosome vesicles. The resistance of glycoRNA-containing exosomes to RNase treatment suggests that Ac4GalNAz-derived glycoRNA constitutes intraluminal cargo, distinct from recently reported cell surface glycoRNAs. Furthermore, we demonstrate that exosome cargo can be transferred to naive cells, underscoring exosome-mediated intercellular communication of glycoRNAs. Inhibition of exosome biogenesis leads to the accumulation of intracellular glycoRNA while blocking glycan transfer to proteins concomitantly reduced the targeting of glycoRNA within exosomes. These findings highlight a correlation between protein and RNA glycosylation, suggesting that the accumulation of glycoRNAs within exosomes is a regulated process. Our results support a functional role for glyco-modification in mediating RNA targeting into exosomes, offering new insights for enhancing recent advances in exosome-directed diagnostics and therapeutic applications.

cell biology↗