Biology subjects

Yu, T.

Publications and source records attributed to Yu, T..

At least 37 records · Page 2Linked to original sources

bioRxiv2025

Primate-specific adaptation of Ku protects transcriptomic integrity by suppressing Alu-mediated alternative splicing

Accurate pre-mRNA splicing is essential for the transfer of genetic information but faces unique challenge in higher primates due to the massive expansion of intronic Alu elements1-3. While studying Ku, the Ku70/Ku80 heterodimer best known for initiating non-homologous end-joining (NHEJ) by encircling DNA ends4, we discovered that Ku expression increased markedly during primate evolution in parallel with Alu expansion5. Ku binds double-stranded RNA (dsRNA) stem-loops, including those at the antisense Alu (asAlu) elements within introns5. Here, we show that Ku-depletion in human cells has a broad impact on splicing largely independent of cell-cycle states, NHEJ, or innate immune signaling, significantly affecting ~8-10% of quantifiable alternative splicing events. Mechanistically, Ku directly binds exonic asAlu to prevent their aberrant inclusion and binds asAlu within inverted-repeat Alu (irAlu) pairs flanking canonical exons to prevent exon skipping6. Among human tissues, Ku expression in the brain is consistently ~50% lower, correlating with more permissive expression of Alu-derived splice variants, particularly those encoding mitochondrial proteins and RNA-binding factors. Correspondingly, heterozygous Ku loss in patient causes developmental delay, neurological dysfunction, and acidosis. Together our findings identified Ku as a critical suppressor of Alu-associated alternative splicing co-opted during evolution with implications for primate brain function and human disease.

molecular biology↗

bioRxiv2025

Genomic Structural Variation Underlies Cell-Type-Specific Betacyanin Variegation in Chenopodium quinoa

The allotetraploid crop quinoa (Chenopodium quinoa) accumulates red/violet betacyanins, which function as vital stress-mitigating antioxidants. We investigated the genetic basis of red/green variegation observed in the aerial organs of the P0429 accession. We demonstrated that this color mosaic is primarily localized to the epidermal bladder cells (EBCs), with red EBCs accumulating [~]50-fold higher betacyanin levels than colorless EBCs. Cell-type-specific RNA-sequencing of EBCs identified the cytochrome P450 gene Cqu0091301 (CYP76AD) as the dominant and rate-limiting factor, exhibiting strong upregulation in red EBCs. This high pigmentation requires a specific structural variation in the P0429 accession: a [~]4-kb genomic insertion that restores the full functionality of Cqu0091301, which is otherwise truncated and non-functional in common reference genomes. Genomic analysis reveals that Cqu0091301 is part of a CYP76AD-DODA gene cluster. Notably, expression analysis revealed functional divergence between the quinoa subgenomes, with B-subgenome CYP76AD genes highly dominant in EBCs, while A-subgenome homologs were preferentially expressed in other tissues. Our results establish a clear link between structural genomic variation and cell-type-specific betalain biosynthesis, providing molecular insight into pigment regulation and subgenome specialization in allotetraploid quinoa.

plant biology↗

bioRxiv2025

Differential targeting of human pyroptotic Caspase-5 and Caspase-4 by Shigella OspC2 and OspC3

Pyroptosis is an inflammatory cell death pathway that is a key defense mechanism of intestinal epithelial cells. To successfully establish an infection, intracytosolic Gram-negative pathogens must block this host response. Indeed, Shigella OspC3 suppresses epithelial pyroptosis by targeting and inactivating Caspase-4 (CASP4). Here, we demonstrate that OspC2, which shares 96% identity with OspC3, targets Caspase-5 (CASP5), a close paralog of CASP4. Through a combination of yeast two-hybrid, transfection, and bacterial infection assays, we show that the distinct pyroptotic caspase specificities of OspC2 and OspC3 are determined by a short -helical region, designated the Pyroptotic Caspase Specificity (PCS) domain. This domain is located upstream from the Ankyrin Rich Repeat (ARR) region previously established to promote OspC3 binding to CASP4. Swapping PCS domains between OspC2 and OspC3 is sufficient to redirect their caspase targeting. Evidence for CASP5-driven pyroptosis in response to infection has not yet been established. However, CASP5 displays signatures of positive selection at residues predicted to interact with the PCS domain of OspC2. Notably, the introduction of orangutan-specific residues into human CASP5 disrupt its interaction with and modification by OspC2, demonstrating that CASP5 natural variation can cause key functional differences in this host-microbe molecular interaction. These findings highlight the evolutionary interplay between bacterial effectors and host proteins, support a likely role for CASP5 in responding to Gram-negative bacteria, and identify promising therapeutic targets for enhancing epithelial defense against bacterial pathogens. ImportanceShigella species are human-specific Gram-negative pathogens that establish a replicative niche in intestinal epithelial cells by blocking pyroptosis, a key inflammatory cell death pathway. We reveal that two closely related Shigella type III secreted effectors, OspC2 and OspC3, specifically inactivate the human caspase paralogs CASP5 and CASP4, respectively. This specificity is determined by their newly identified Pyroptotic Caspase Specificity (PCS) domains. In addition, we find that positively selected residues in CASP5 alter the OspC2/CASP5 interaction, underscoring the impacts of ongoing evolutionary arms races between bacterial effectors and host immune proteins. By elucidating the molecular basis of caspase targeting and adaptation, this work provides new insight into the diversification of host defense mechanisms and identifies potential therapeutic targets for enhancing epithelial resistance to bacterial infection.

microbiology↗

bioRxiv2025

Neat1 alleviates ischemic injury in skeletal muscles

Peripheral artery disease (PAD) has historically been regarded as an age-related vascular disorder; however, recent attention has shifted toward the myopathic components of the disease. Conventional interventions, such as revascularization, have had limited success in reversing muscle pathology or preventing adverse outcomes like amputation. Hypoxia-inducible factors (HIFs) are key regulators of cellular responses to ischemia, including the promotion of angiogenesis and glycolysis. While pharmacological stabilization of HIF proteins represents a promising therapeutic strategy, its efficacy is diminished in aged muscles due to their intrinsically low basal HIF expression. We hypothesized that long noncoding RNAs (lncRNAs) might enhance the hypoxic response in aged muscle through post-transcriptional regulation of HIF expression. Our study identified a long noncoding RNA Neat1, as a critical mediator of the hypoxia-induced stress response, including upregulation of Hif1. In a murine hindlimb ischemia model, Neat1 knockout mice exhibited extensive necrosis following femoral artery ligation, whereas Neat1 overexpression conferred protection against ischemic injury. Mechanistically, we found that Neat1 regulates the stability of Hif1a mRNA, as Hif1a transcript levels were significantly reduced in Neat1-deficient muscle cells. Importantly, aged muscles displayed a blunted hypoxic response due to diminished Hif1a expression--an effect that was reversed through Neat1 overexpression, resulting in improved resistance to ischemic damage. In summary, our findings highlight Neat1 as a novel regulator of muscle adaptation to hypoxia in aging. Enhancing Neat1 expression may represent a promising therapeutic strategy for improving ischemic outcomes in patients with peripheral artery disease.

cell biology↗

bioRxiv2025

A gap-free telomere-to-telomere pig reference genome provides insight in centromere evolution and breed-specific selection

The domestic pig is a key agricultural species and biomedical model, yet its reference genome has remained incomplete. Using PacBio HiFi, Oxford Nanopore reads, and Hi-C sequencing, we assembled the first telomere-to-telomere (T2T), gap-free pig genome (T2T-Sscrofa). Importantly, this assembly derives from the same individual pig that provided the original reference genome, thereby completing the long-standing foundation of pig genomics. This assembly resolves 274.8 Mb of previously unassembled sequence, including centromeres, segmental duplications, and ribosomal DNA arrays, and identifies 255 new protein-coding genes. Comparative analyses reveal a Robertsonian translocation in the western European wild boar and extensive structural variation across global pig populations. T2T-Sscrofa provides a comprehensive genomic foundation for agricultural, evolutionary, and biomedical research.

zoology↗

bioRxiv2025

Knowledge-Driven Interpretable Neural Networks for Mechanistic Insight

Analyzing omics data based on pathway knowledge is critical for understanding the molecular mechanism behind pathological changes, but current pathway analysis methods do not model the detailed mechanistic nature of biological interactions, limiting the understanding of pathway behavior to a relatively shallow level. To address this issue, we present a knowledge-driven machine learning framework that embeds features into pathway graphs and models reactions analytically, producing interpretable feature hierarchies and sub-networks where functional associations are estimated to model biological interactions. The approach is agnostic to feature selection, enabling the use of full omics datasets without discarding weak signals. Applications to breast cancer microRNA-gene regulation data and COVID-19 metabolomics data highlight immune and metabolic pathways relevant to disease progression. This framework bridges predictive modeling with mechanistic interpretation, offering a foundation for integrative pathway analysis.

bioinformatics↗

bioRxiv2025

NicheScope: Identifying Multicellular Niches and Niche-Regulated Cell States in Spatial Transcriptomics

The functional state of a cell is intrinsically linked to its local microenvironment, or cell niche, a complex milieu formed by multiple interacting cell types. Deciphering how these multicellular niches regulate cell states is fundamental to understanding tissue biology and disease mechanisms, yet remains challenging with current computational approaches. Here, we present NicheScope, a computational framework for transcriptome-wide identification and characterization of Multicellular Niches (MCNs) and their corresponding Niche-Regulated Cell States (NRCSs) from spatial transcriptomics data. NicheScope operates on the principle that a cells transcriptional state is associated with its local multicellular composition. It employs a robust statistical approach to jointly model neighborhood composition and transcriptome-wide gene expression, enabling the simultaneous discovery of MCNs, defined by specific combinations of neighboring cell types, and their associated NRCSs, characterized by distinct gene programs. We demonstrate NicheScopes power and versatility across diverse tissues and platforms, including lymph node, lung adenocarcinoma, and head and neck cancer. NicheScope reproducibly dissected established tissue structures in lymph nodes across tissue regions and platforms, uncovered clinically relevant tumor cell-associated MCNs in lung adenocarcinoma, and revealed shared and condition-specific MCNs in primary and metastatic tumors. Our results establish NicheScope as a powerful, robust, scalable, and interpretable framework for dissecting the spatial and functional organization of complex tissues, providing new insights into multicellular coordination in health and disease.

bioinformatics↗

bioRxiv2025

Transcription factor NFYA directs male meiotic entry by facilitating accessible chromatin at meiotic promoters in mice

Meiotic prophase I characterized by homologous recombination and synapsis is an intricate step for spermatogenesis. This process entails extensive changes to chromatin and transcription. Prior to prophase I, accessible chromatin bound by paused Pol II at meiotic gene promoters is essential for their timely activation later during meiosis. However, the factor responsible for promoting accessible chromatin at meiotic gene promoters before entry into prophase I is unknown. Here, we discovered that NFYA expressed in pre-meiotic germ cells promotes accessible chromatin at meiotic gene promoters including those regulated by STRA8/MEISON axis. Concordantly, conditional germline deletion of Nfya in male mice blocks meiotic entry. Functionally, our spatial and single-cell ATAC-seq data revealed that loss of NFYA in pre-meiotic cells disrupts accessible chromatin at meiotic gene promoters. Our study identifies a pioneer role for NFYA in facilitating accessible chromatin at meiotic gene promoters before meiosis, thereby regulating the timely activation of meiotic genetic program.

developmental biology↗

bioRxiv2025

GLASS: A Graph Learning Algorithm for Screening Splice-Aware Alignments of Long-Read RNA-seq

With the continuous development of third-generation RNA-seq, obtaining accurate splice-aware alignments for the long RNA-seq reads to reference genomes has become one of the major challenges in transcriptomic analysis. To mitigate the erroneous alignments arising from existing long-read RNA-seq aligners, we propose GLASS, a novel splice-aware alignments filtering approach based on third-generation transcriptome data. GLASS introduces a newly designed Read-AS Map model and integrates graph machine learning techniques for detecting and removing falsely spliced aligned reads from alignment files. Experimental results demonstrate that GLASS significantly reduces the error rate of spliced alignmnt and enhance the accuracy of subsequent transcriptome reconstruction. Additionally, GLASS demonstrates strong generalization ability in data from species such as Mus musculus and Arabidopsis thaliana, providing a new approach for the efficient processing of third-generation transcriptome data and offering more reliable data support for subsequent gene expression analysis and functional studies.

bioinformatics↗

bioRxiv2025

Atrophin-1 Antisense Oligonucleotide Provides Robust Protection from Pathology in a Fully Humanized DRPLA Model

Dentatorubral-pallidoluysian atrophy (DRPLA) is a fatal neurodegenerative disease arising from a CAG repeat expansion in the atrophin-1 (ATN1) gene. Because DRPLA, like many repeat expansion disorders (REDs), arises predominantly from toxic gain-of-function mechanisms, we hypothesized that ATN1 knockdown would have therapeutic potential. To test this, we established the first fully-humanized mouse model of a RED, in which one allele of mouse Atn1 is completely replaced by human ATN1, including 112 pure CAG repeats. This novel approach to exploring RED biology provides significant advantages, notably the ability to test sequence-specific therapeutics targeting human sequences, even in introns and untranslated regions of pre-mRNA. We found that our model--the Atn1Q112/+ mouse--recapitulates key features of human DRPLA, including behavioral alterations, reduced brain size and aggregate accumulation. We treated Atn1Q112/+ mice with antisense oligonucleotides (ASOs) targeting mouse Atn1 (to probe for loss of function concerns), human ATN1, or a combination. Treatment with human, but not mouse, ATN1-targeting ASOs provides remarkable protection from a range of disease-related behavioral phenotypes, including aggregation of mutant ATN1 (mATN1), and marked rescue of transcriptional dysregulation in the cerebellum. These results have helped motivate an ongoing human clinical study of ASOs targeting ATN1 for DRPLA.

neuroscience↗

bioRxiv2025

Predictable Engineering of Signal-DependentCis-Regulatory Elements

Cis-regulatory elements (CREs) control how genes respond to external signals, but the principles governing their structure and function remain poorly understood. While differential transcription factor binding is known to regulate gene expression, how CREs integrate the amount and combination of inputs to secure precise spatiotemporal profiles of gene expression remains unclear. Here, we developed a high-throughput combinatorial screening strategy, that we term NeMECiS, to investigate signal- dependent synthetic CREs (synCREs) in differentiating mammalian stem cells. By concatenating fragments of functional CREs from genes that respond to Sonic Hedgehog in the developing vertebrate neural tube, we found that CRE activity follows hierarchical design rules. While individual 200-base-pair fragments showed minimal activity, their combinations generated thousands of functional signal-responsive synCREs, many exceeding the activity of natural sequences. Statistical modelling revealed CRE function can be decomposed into specific quantitative contributions in which sequence fragments combine through a multiplicative rule, tuned by their relative positioning and spacing. These findings provide a predictive framework for CRE redesign, which we used to engineer synthetic CREs that alter the pattern of motor neuron differentiation in neural tissue. These findings establish quantitative principles for engineering synthetic regulatory elements with programmable signal responses to rewire genetic circuits and control stem cell differentiation, providing a basis for understanding developmental gene regulation and designing therapeutic gene expression systems.

developmental biology↗

bioRxiv2025

LOCATE: using Long-read to Characterize All Transposable Elements

Transposons constitute [~]45% of the human genome, driving gene evolution and contributing to disease, but their repetitive nature complicates the identification of new insertions. We present LOCATE (Long-read to Characterize All Transposable Elements), an algorithm using long-read sequencing to detect and assemble transposon insertions. LOCATE outperforms existing tools on simulated datasets and achieves the best performance in two previous benchmarks, as well as in a new benchmark we constructed using real biological datasets. Applying LOCATE to public datasets revealed that pre-existing Alu copies create two hotspots for Alu and LINE1 insertions: the A-rich linker and the poly(A) tail. We further observed a preference for self-insertions over non-self-insertions in Alu and LINE1, suggesting a "feedforward" transposition mechanism in which Alu and LINE1 RNA transcripts target the hotspots of their source copies to generate new insertions. LOCATE enhances our ability to study transposons and their role in genome dynamics.

bioinformatics↗

bioRxiv2025

Tissue reassembly with generative AI

The spatial arrangement of cells is fundamental to their function, but single-cell RNA sequencing loses spatial context by dissociating cells from tissues. We present LUNA, a generative AI model that reassembles dissociated cells into tissue structures solely from gene expression by learning spatial priors from existing spatially resolved datasets. We apply and validate LUNA across multiple technologies including reconstructing the MERFISH whole mouse brain atlas with over 1.2 million cells, de novo reassembly of mouse central nervous system scRNA-seq atlas and inference of the spatial locations of nuclei lost during Slide-tags profiling. Furthermore, we show that LUNA generalizes to unseen cell types and to pathological samples in the Parkinsons disease mouse model, identifying regions of change due to pathology. We envision that AI-driven tissue reassembly can help to overcome current technological limitations and advance our understanding of tissue organization and function.

bioinformatics↗

bioRxiv2025

A Generalized Platform for Artificial Intelligence-powered Autonomous Protein Engineering

Proteins are the molecular machines of life with numerous applications in energy, health, and sustainability. However, engineering proteins with desired functions for practical applications remains slow, expensive, and specialist-dependent1-3. Here we report a generally applicable platform for autonomous protein engineering that integrates machine learning and large language models with biofoundry automation to eliminate the need for human intervention, judgement, and domain expertise. Requiring only an input protein sequence and a quantifiable way to measure fitness, this autonomous platform can be applied to engineer virtually any protein. As a proof of concept, we engineered Arabidopsis thaliana halide methyltransferase (AtHMT)4 for a 90-fold improvement in substrate preference and 16-fold improvement in ethyltransferase activity, along with developing a Yersinia mollaretii phytase (YmPhytase)5,6 variant with 26-fold improvement in activity at neutral pH. This was accomplished in four rounds over four weeks, while requiring construction and characterization of fewer than a total of 500 variants for each enzyme. This platform for autonomous experimentation paves the way for rapid advancements across diverse industries, from medicine and biotechnology to renewable energy and sustainable chemistry.

synthetic biology↗

bioRxiv2024

Non-invasive diagnosis of early chronic colitis cancerization via amplified sensing of miRNA-21 in NIR-IIb window

Early diagnosis of the colitis-associated colorectal cancer (CRC) is of great significance for improving prognosis and survival rates. However, the clinical used colonoscopy and biopsy methods are invasive and lack of sensitivity at early stage of cancerization. Herein, we present an amplified sensing strategy in the second near-infrared b (NIR-IIb, 1500-1700 nm) window for non-invasive in situ visualization of early cancerization biomarker miRNA-21. A CRC nanosensor composed of Er3+ doped lanthanide nanoparticles, DNAzyme, and IR820 dye is designed as a NIR-IIb ratiometric luminescence reporter, providing rapid feedback and high sensitive miRNA-21 detection with limit of detection (LOD) of 1.26 pM. This strategy enables a non-invasive detection of colitis-associated cancerization up to [~]4 weeks ahead of the clinically used biopsy analysis, providing a promising alternative for early diagnosis of chronic colitis cancerization and guidance for therapeutic management.

bioengineering↗

bioRxiv2024

Deaminase-mediated chromatin accessibility profiling with single-allele resolution

Binding of transcription factors (TFs) at gene regulatory elements controls cellular epigenetic state and gene expression. Current genome-wide chromatin profiling approaches have inherently limited resolution, complicating assessment of TF occupancy and co-occupancy, especially at individual alleles. In this work, we introduce Accessible Chromatin by Cytosine Editing Site Sequencing with ATAC-seq (ACCESS-ATAC), which harnesses a double-stranded DNA cytosine deaminase (Ddd) enzyme to stencil TF binding locations within accessible chromatin regions. We optimize bulk and single-cell ACCESS-ATAC protocols and develop computational methods to show that the increased resolution compared with ATAC-seq improves the accuracy of TF binding site prediction. We use ACCESS-ATAC to perform genome-wide allelic occupancy and co-occupancy imputation for 64 TFs each in HepG2 and K562, revealing that the propensity of a majority of TFs to co-occupy nearby motifs oscillates with a period approximating the helical turn of DNA. Altogether, ACCESS-ATAC expands the resolution and capabilities of bulk and single-cell epigenomic profiling.

genomics↗

bioRxiv2024

Mapping targetable sites on the human surfaceome for the design of novel binders

The human cell surfaceome, integral to cell communication and disease mechanisms, presents a prime target for therapeutic intervention. De novo protein binder design against these cell surface proteins offers a promising yet underexplored strategy for drug development. However, the vast search space and limited data on natural or competitive binders have historically limited experimental success. In this study, we systematically analyzed the entire human surfaceome, identifying approximately 4,500 targetable sites and introducing high-quality binder seeds tailored for protein design applications. To validate these seeds, we implemented two experimental approaches (protein scaffolding and peptide cyclization) on three representative targets (FGFR2, IFNAR2, and HER3). Our results revealed a high success rate, emphasizing the precision and therapeutic potential of these seeds, as well as the need for constant improvements of computational protein design pipelines utilizing machine learning and physics-based methods. Additionally, we present SURFACE-Bind, an interactive database offering open access to all generated data. The high-throughput computational design methods and target-specific binder seeds established here pave the way for a new generation of targeted therapeutics for the human surfaceome.

synthetic biology↗

bioRxiv2024

STING agonists drive recruitment and intrinsic type I interferon responses in monocytic lineage cells for optimal anti-tumor immunity

The cyclic GMP-AMP synthase-stimulator of interferon genes (cGAS-STING) pathway, a sensor of cytosolic DNA, orchestrates the production of pro-inflammatory cytokines, chemokines, and type I interferons (IFN-I), thereby contributing to spontaneous tumor surveillance. Intratumoral delivery of synthetic STING agonists induces IFN-I dependent tumor regression in preclinical cancer models and is being tested clinically. In this study, we investigate the role of monocytic lineage (MCs) cells in response to STING agonist induced IFN-I signaling. We show that CCR2-deficient mice, lacking inflammatory MCs in the periphery, or Lyz2-Cre-IFNAR1fl/fl mice in which IFN-I signaling in monocytes is reduced, exhibit impaired responses to STING agonist therapy of MC38 and/or B16F10 tumors. STING agonist treatment induced CCR5-dependent migration of MCs carrying tumor antigen from the tumor to the lymph nodes. Single-cell RNA sequencing of CD45+ cells from lymph nodes and tumors of mice in which half the hematopoietic cells lack the interferon alpha/beta receptor 1 (IFNAR1) revealed that STING agonist therapy induces intrinsic IFNAR1-dependent acquisition of an inflammatory monocytic cell phenotype distinct from inflammatory cDC and a reduction in macrophages with a pro-tumor TGF{beta}/angiogenesis transcriptome. IL-18 - IL-18R1 interaction was the top predicted interaction between monocytic lineage cells and CD8+T cells or NK cells. Blocking IL-18 reduced IFN-{gamma} production by CD8 T cells in LNs and decreased the therapeutic efficacy of STING agonist treatment in CCR2+/+ but not in CCR2-/- mice. These findings support a pivotal role for IL-18 producing inflammatory monocytic lineage cells in CD8 T cell control of melanoma following STING agonist treatment.

immunology↗