Biology subjects

Yu, C.

Publications and source records attributed to Yu, C..

At least 55 records · Page 3Linked to original sources

bioRxiv2025

RNA decay via the nuclear exosome is essential for piwi-mediated transposon silencing

Nuclear Argonaute proteins safeguard genome integrity by directing transcriptional silencing and heterochromatin formation at transposon loci. Yet it remains unclear how Argonautes enforce robust repression while relying on target transcription for their own recruitment. Here we show that transposon silencing by the Drosophila nuclear Piwi-piRNA pathway requires degradation of target RNA by the nuclear exosome. Using proximity proteomics at endogenous Piwi target sites, we identify two previously uncharacterized paralogs, TEsup-1 and TEsup-2, as essential cofactors for Piwi-mediated silencing. TEsup proteins act in part by engaging nuclear exosome adaptor complexes at piRNA-targeted transcripts through a domain that recognizes proline-rich peptides. Disruption of the Piwi-TEsup-exosome axis leads to accumulation and nuclear export of piRNA-targeted transposon RNAs. Notably, the P-element--which evades heterochromatin-based repression--is silenced primarily through this RNA-decay pathway. Thus, the nuclear piRNA pathway couples target recognition to RNA degradation, reconciling small RNA-guided heterochromatin formation with ongoing transcription at target loci.

molecular biology↗

bioRxiv2025

Orthosteric Molecular Glue Inhibits COP9 Signalosome with Substrate-Dependent Potency

Orthosteric inhibitors block enzyme active sites and prevent substrates from binding. Enhancing their specificity through substrate dependence seems inherently unlikely, as their mechanism hinges on direct competition rather than selective recognition. Here, we show that a molecular glue mechanism unexpectedly imparts substrate-dependent potency to CSN5i-3, an orthosteric inhibitor of the COP9 signalosome (CSN). We first confirm that CSN5i-3 inhibits CSN, which catalyzes NEDD8 deconjugation from the cullin-RING ubiquitin ligases (CRLs), by occupying the active site of its catalytic subunit, CSN5, and directly competing with the iso-peptide bond substrate. Curiously, the orthosteric inhibitor binds free CSN with only micromolar affinity, yet achieves nanomolar potency in blocking its deneddylase activity. Cryo-EM structures of the enzyme-substrate-inhibitor complex reveal that active site-engaged CSN5i-3 occludes the substrate iso-peptide linkage while simultaneously extending an NEDD8-binding exosite of CSN5, acting as a molecular glue to cement the NEDD8-CSN5 interaction. The cooperativity of this tri-molecular CSN5i-3-NEDD8-CSN5 assembly, in turn, sequesters CSN5i-3 at its binding site, conferring high potency to the orthosteric inhibitor despite its low affinity for the free enzyme. Together, our findings highlight the modest affinity requirements of molecule glues for individual target proteins and establish "orthosteric molecular glue inhibitors" as a new class of substrate-dependent enzyme antagonists.

molecular biology↗

bioRxiv2025

Uncovering the molecular basis of kinase activity and substrate recognition with phospho-PCA

Protein kinases relay information to various cellular processes, and their dysregulation underlies numerous human diseases. Despite their importance, our understanding of how kinase domains and their variants impact protein stability, catalytic activity, and substrate recognition is incomplete. In this work, we develop the phosphorylation protein complementation assay (phospho-PCA), which enables quantitative measurements of kinase-substrate interactions by coupling them to the growth of bud-ding yeast, thereby enabling deep mutational scanning of kinase domains. When combined with deep mutational scans targeting folding stability and Bayesian modeling, phospho-PCA can disentangle the relative impact of mutations on kinase domain stability, catalytic activity, and substrate specificity. We demonstrate the accuracy and breadth of phospho-PCA, showing its applicability to both tyrosine and serine/threonine kinase domains. We then apply our method to three closely related protein kinases with distinct substrate preferences, evaluating over 15,000 kinase variants against a panel of three substrates for both catalytic activity and substrate specificity. The resulting dataset constitutes the largest and most detailed variant-to-function map assembled for this enzyme family to date, revealing numerous mutations that alter kinase activity and substrate specificity. Physics-based modeling reveals how these mutations operate through diverse mechanisms, including long-range allosteric communication, to alter both activity and substrate specificity. Given its scalability, we believe phospho-PCA can measure the functional impact of variants across the entire human kinome.

molecular biology↗

bioRxiv2025

Models for the architecture of the human inner kinetochore CCAN complex on centromeric α-satellite CENP-A nucleosome arrays

Human kinetochores assemble onto centromeric DNA defined by tandem copies of thousands of the 171 bp -satellite repeat sequence. The centromere-specific CENP-A nucleosome (CENP-ANuc) recruits the inner kinetochore constitutive centromere associated network (CCAN) complex. A previous cryo-EM structure of CCAN bound to a CENP-ANuc reconstituted with a 171 bp -satellite repeat sequence showed how extranucleosomal linker DNA threads through an internal tunnel in the CCAN complex. To understand the higher-order architecture of the inner kinetochore assembled onto -satellite repeat arrays, we have determined cryo-EM structures of CCAN with longer DNA sequences. These include free DNA and single and dimeric -satellite repeats with CENP-A nucleosomes. We show from the structures of CCAN bound to both free DNA and monomeric CENP-ANuc that CCAN engages 65-70 bp of DNA comprising 30-35 bp of an upstream -satellite repeat. This upstream DNA interacts with the histone-fold domain subunits of the CENP-TWSX module in a manner resembling how DNA is wrapped in nucleosomes. A complex of CCAN assembled onto a dimeric -satellite repeat with two CENP-A nucleosomes showed that CCAN can only be accommodated on the linker DNA by unwrapping DNA from the CENP-TWSX module together with 25 bp of DNA from the upstream nucleosome. We discuss the implications of these results for models of CCAN assembly on arrays of -satellite chromatin containing CENP-ANuc.

molecular biology↗

bioRxiv2025

Accurate and efficient phylogenetic inference through end-to-end deep learning

Accurate phylogenetic inference is crucial for understanding evolutionary relationships among species. Deep learning technique has been introduced for phylogenetic inference; however, the existing deep learning-based approaches either suffer from limited accuracy as they split inference into several disjoint stages, or exhibit low efficiency and hardly apply to the cases with over 20 species. Here we present an accurate and efficient approach to phylogenetic inference. Our approach, called NeuralNJ, employs an end-to-end framework that directly constructs phylogenetic trees from the input taxa, thus effectively avoiding the inaccuracy incurred by the split inference stages. The key innovation of NeuralNJ lies in its learnable neighbor joining mechanism, which iteratively joins neighbors guided by learned priority scores and thereby achieves accurate tree reconstruction. The inference accuracy is further enhanced through incorporating reinforcement learning-based tree search. Using both simulated and empirical data as representatives, we demonstrate that NeuralNJ can effectively infer phylogenetic tree with improved computational efficiency and reconstruction accuracy. The study paves the way to accurate and efficient phylogenetic inference for hundreds of taxa in complex evolutionary scenarios.

bioinformatics↗

bioRxiv2025

Hippocampal theta sweeps indicate goal direction

Successful spatial navigation requires rapid evaluation of potential future trajectories. Hippocampal "theta sweeps", sequential activation of place cells within individual theta cycles, exhibit predictive dynamics within the ideal timeframe to fulfill this role. However, whether these sequences simply reflect movement-related variables or afford more cognitive goal-directed planning remains unresolved. Using data from a navigation task on the "Honeycomb" maze that allows dissociation of head-, movement- and goal-direction correlates, we found that hippocampal theta sweeps exhibit robust goal-oriented directional biases, independent of movement- or head-direction. An existing model of theta sweeps, with an additional goal-oriented directional input, reproduces these findings and predicts goal-oriented theta phase precession, which we confirm empirically. Replay events during immobility-related sharp wave/ripples are also goal-directed, and therefore more aligned with theta sweeps than experience. Our findings indicate that hippocampal theta sweeps provide a neural substrate for online goal-directed spatial planning.

neuroscience↗

bioRxiv2025

Integrated spatial proteomics of human PDAC uncovers an expanded tumour-immune-stroma spectrum with genomic associations

Distinctively, pancreatic ductal adenocarcinoma (PDAC) consists of sparse tumour lesions intertwined with extensive desmoplastic stroma. The complexity of tumour-microenvironment interactions within this desmoplasia poses a challenge for accurate tumour profiling and patient stratification, and characterizes a profoundly chemoresistant tumour. Here we mapped the spatial relationships between tumour, stroma, and immune cell compartments delineating tumour and microenvironment types that expand the classical to basal spectrum of human PDAC. We used imaging mass cytometry to profile the in situ multi-cellular organization of 81 cell types in resected cases with paired whole genome sequencing. Cell types, functions, and pathway activation were distributed as highly reproducible environments in discrete locations throughout these tumours, which we deep-profiled using laser-capture mass spectrometry. We show that the connections between tumour phenotypes, vascularization, immune response, and stromal biophysical state are reinforced by genomic aberrations, altered by treatment, and associated with patient outcome. Predictive machine-learning models showed that spatial single cell data outperformed genomic or clinical features but integrated multi-omics models provide the best prediction of patient survival with compressed models requiring only 10 non-redundant robust molecular measures associated with the phenotypic spectrum of PDAC. Together, these findings define a phenotypic and molecular framework of PDAC that captures tumour-microenvironment co-dependencies and offers a refined basis for patient stratification and therapeutic targeting.

cancer biology↗

bioRxiv2025

LENG8 mediates RNA nuclear retention and degradation in eukaryotes

In eukaryotes, incompletely processed and misprocessed mRNAs as well as numerous noncoding RNAs are retained in the nucleus and often degraded. However, the mechanisms for this critical quality control pathway remain poorly understood. Here we identify LENG8 as a conserved RNA nuclear retention factor. We showed that LENG8 is recruited to pre-mRNAs by splicing factors, including the U1 snRNP. LENG8 binds to PCID2 and SEM1 to form the REX (Repressor of EXport) complex, which is conserved from yeast to human, and causes RNA nuclear retention by acting as a dominant negative factor for the essential mRNA export factor TREX-2. LENG8 depletion leads to the leakage of misprocessed mRNAs, including intronically polyadenylated and intron-retained mRNAs, as well as noncoding RNAs into the cytoplasm. Finally, LENG8 promotes RNA degradation by recruiting PAXT and the RNA exosome. Thus our study revealed a conserved quality control mechanism for eukaryotic gene expression that ensures only fully and correctly processed RNAs are exported from the nucleus.

molecular biology↗

bioRxiv2025

The Cornea Harbors a Tricellular Neuro-Immune Niche that Underpins Touch Sensation

Piezo2 is a mechanosensitive ion channel essential for touch and proprioception, yet the mechanisms that maintain this sensory modality in adult tissues are unknown. Using multiphoton imaging of the cornea in live mice, we discovered that the Cx3cr1Cre locus targets not only macrophages, but also a distinct subset of nerves. Spatial-RNAseq resolved that Cx3cr1Cre-driven labeling was uniquely enriched in Piezo2-expressing neurons, a result of temporal Cx3cr1 expression during development. Through lineage tracing, scRNAseq, and imaging, we identified a novel tripartite cellular niche at the epithelial basement membrane, comprised of monocyte-derived macrophages, nerves, and Schwann cells. Additional scRNAseq and genetic studies revealed that Schwann cell-derived IL34 maintained corneal macrophages. Through pharmacologic and genetic perturbations, we also demonstrate corneal macrophages selectively maintained the structure-function of Piezo2-enriched nerve endings, with disruption of this niche causing specific deficits in mechanosensation while preserving other sensory modalities. Altogether, we describe a novel tricellular niche in the cornea required for Piezo2-mediated touch sensation, suggesting new directions for investigating mechanosensory circuits including proprioception.

immunology↗

bioRxiv2025

Directed cell migration is a versatile mechanism for rapid developmental pattern formation

The evolution of multicellular organisms hinges on self-organization mechanisms that generate tissues with diverse functions. A central process is the breaking of symmetry to form spatial patterns from initially uniform conditions. Among the various mechanisms proposed, directed cell migration--driven by chemotaxis, durotaxis, differential adhesion or other processes--offers a compelling strategy to organize tissues rapidly and robustly. Here, we unify these concepts into a general mathematical framework and show that it can produce diverse spatial patterns across one-, two-, and three-dimensional domains. Using numerical simulations and stability theory, we characterize the emergence, geometry, and formation speed of these patterns. Our findings provide a mechanistic understanding of morphogenesis beyond the traditional chemical or mechanical patterning paradigms and offer a quantitative foundation to guide pattern formation in tissue engineering and regenerative medicine.

developmental biology↗

bioRxiv2025

Dysfunction of microglia-mediated synaptic pruning in Autism spectrum disorder

Autism spectrum disorder (ASD) has been increasingly associated with abnormalities in synaptic pruning. Although significant progress has been made in elucidating the genetic and immunological underpinnings of ASD, its core pathological mechanisms remain poorly understood. In this study, we developed a network model integrating the in flammatory response pathway in microglia with synaptic signaling pathway to investigate how lipopolysaccharide (LPS) and synaptic activity jointly regulate microglia-mediated synaptic pruning. Our results reveal that pro-in flammatory activation of microglia impairs pruning efficiency under reduced synaptic activity, leading to excessive synaptic accumulation particularly in the prefrontal cortex and contributing to ASD-like phenotypes. Conversely, enhanced synaptic activity partially suppresses LPS-induced synaptic apoptosis and promotes synaptic retention. These findings suggest multiple therapeutic strategies, including targeting pruningrelated molecular pathways, mitigating neuroinflammation, and modulating synaptic excitability to alleviate ASD symptoms.

systems biology↗

bioRxiv2025

Prenatal liver is resistant to low glucose-induced inhibition of mTORC1

Prenatal development may adopt unique patterns of metabolic responses to different nutrient supplies. AMPK and mTOR are two central metabolic regulators, with AMPK acting to slow down and mTOR to promote anabolism. Typically, low glucose inhibits TRPVs, leading to AMPK activation and mTOR complex I (mTORC1) inhibition. Here, we observed surprisingly that mTORC1 in the foetal liver remains active in low glucose, although AMPK is effectively activated in an AMP-dependent manner. Mechanistically, we found that TRPV4, a key liver TRPV, is acetylated at K608, disabling its inactivation by fructose-1,6-bisphosphate (FBP)-unoccupied aldolase. Mutation of K608 to arginine renders TRPV4 able to respond to low glucose in foetal hepatocytes. Consistently, embryonic liver-specific expression of acetylation-defective TRPV4-K608R mutant led to mTORC1 inhibition, and caused abnormal intrauterine development or even foetal death. Our findings reveal that the TRPV-mediated resistance of mTORC1 inhibition in low glucose acts as a safeguard for normal foetal development.

biochemistry↗

bioRxiv2025

Architecture and Function of Holocentric CENP-A-Independent Kinetochores

Kinetochores are essential macromolecular complexes that anchor chromosomes to the mitotic spindle to ensure faithful cell division1. Despite their critical role, the structural organization of kinetochores assembled on centromeres with vastly distinct architectures across diverse species remains poorly understood2,3. To address this question, we determined the cryo-EM structures of the inner kinetochore (CCAN) from the silkmoth Bombyx mori, an insect that lacks the canonical centromere-specifying histone variant CENP-A and exhibits chromosome-wide centromeric activity (holocentric). Our analysis reveals that B. mori CCAN assembles via atypical histone-fold protein dimerization into a self-contained, head-to-head dimer that topologically entraps and loops DNA, creating a point-centromere-like architecture. This structure also incorporates four previously uncharacterized Centromeric Subunit proteins that are evolutionarily repurposed from the outer kinetochore Dam1/DASH complex. Our work establishes this self-contained CCAN dimer as a key structural unit that forms the basis of a holocentric organization and suggests that large-scale centromere architectures can emerge from the modular arrangement of such discrete kinetochore units.

cell biology↗

bioRxiv2025

Intrinsic higher potency of basal urothelial cells to intermediate and umbrella cells as the cell of origin for bladder cancer

Transcriptome profiling of bladder cancer has revealed distinct basal-like and luminal-like molecular subtypes, which may be correlated with pathological subtypes of different patient outcomes. However, whether these molecular subtypes originate from the corresponding cell types in the normal urothelium and whether different cells of origin influence bladder cancer progression remain unclear. Here, we conducted cell-type-specific lineage tracing in CRISPR/Cas9-induced mouse bladder cancer models of Pten and Trp53 targeting. We show that although basal, intermediate, and superficial umbrella cells can all serve as the cell of origin for bladder cancer, transformed umbrella cells were gradually displaced by tumor cells from inner layers, particularly transformed basal cells, which had highest stemness. Histological and single cell RNA-sequencing data comparing basal- and intermediate-cell-induced bladder tumors revealed that basal-induced tumors displayed higher heterogeneity, and contained unique cell clusters including Krt14+Ki67+ highly proliferative basal cells, squamous cell carcinoma, and transitioning cells towards the Gata3+ luminal subtype. Trajectory analysis confirmed the cell lineage differentiation hierarchy uncovered in lineage tracing. Moreover, human bladder cancer molecular subtype signatures were highly enriched in mouse tumor cell clusters of the corresponding cell of origin, and a gene signature derived from the unique basal-induced clusters is predictive of worse patient outcome. Overall, our results support that the basal and luminal molecular subtypes of bladder cancer have the corresponding cells of origin as their basis, and that urothelial basal cells are intrinsically more competitive than intermediate and umbrella cells in generating aggressive bladder cancer subtypes.

cancer biology↗

bioRxiv2025

Taurine Transporter SLC6A6 Expression Promotes Mesenchymal Stromal Cell Function

Mesenchymal stromal cell (MSC) differentiation is critical for the development, maintenance, and repair of bone tissue. This occurs within the bone marrow microenvironment, which consists of various stromal populations and structural components that support skeletal growth, repair and homeostasis. MSCs also promote self-renewal of hematopoietic stem cells and regulate their differentiation. Analysis of our own and publicly available single-cell RNA sequencing datasets of the murine non-immune bone and bone marrow indicates that Slc6a6 expression is enriched in MSCs. Slc6a6 encodes for an ion-dependent transporter of taurine (TauT). Although taurine supplements have been shown to mitigate the onset of bone defects in aged populations, the absence of TauT expression in osteolineage cells suggests that taurines effect on bone may be secondary to its function in other populations, such as MSCs. Using young TauT genetic loss-of-function murine models we find that TauT loss impacts MSC populations in vivo and impairs MSC osteogenic differentiation in vitro. This correlates with decreased bone mineral density and bone strength in young TauT knockout mice. Importantly, shRNA-based knockdown of SLC6A6 expression in primary human MSCs reduces osteogenic differentiation, indicating a key role of taurine uptake in human MSC function. Consistent with a decline in MSC function with TauT loss, we find that TauT null MSCs are unable to support self-renewal and expansion of co-cultured hematopoietic stem/progenitor populations. Mechanistically, our RNA-sequencing analysis identifies downregulation of Wnt/beta-catenin signaling in MSCs in the absence of TauT. These cells also show reduced oxidative phosphorylation, and increased ROS levels, indicating that impaired Wnt signaling and elevated oxidative stress may contribute to the observed defects in osteogenic differentiation capacity. Collectively, our data identify taurine uptake as a key regulator of mesenchymal stromal cell maintenance and osteogenic fate determination.

cell biology↗

bioRxiv2025

Ataxin-2 preserves oocyte genome integrity by promoting timely premeiotic DNA replication

The faithful reassortment and transmission of chromosomes across generations is fundamental to species survival. While much is known about chromosome pairing and recombination, the upstream regulators controlling entry into the meiotic program remain largely elusive. In many species, including Drosophila and mammals, the decision to enter meiosis occurs prior to premeiotic DNA replication and is governed by post-transcriptional regulation, by yet to be discovered factors. Here, we identify the RNA-binding protein Ataxin-2 as a crucial and previously unrecognized regulator of meiotic entry. We show that Ataxin-2 acts post-transcriptionally to promote the entry into meiosis by downregulating the conserved cell cycle inhibitor Dacapo, the Drosophila ortholog of p21/p27. In the absence of Ataxin-2, germ cells mis-regulate Dacapo leading to delayed premeiotic DNA replication and sterility. Strikingly, when DNA replication is delayed and extends into the next stage of meiosis, synaptonemal complex formation, oocytes incur severe genomic DNA damage, likely caused by collisions between replication forks and the synaptonemal complex. Our findings establish Ataxin-2 as a pivotal factor in regulating premeiotic DNA replication and safeguarding oocyte genome stability, shedding new light on the intricate regulatory mechanisms that ensure successful meiosis and fertility.

genetics↗

bioRxiv2025

Continuous flashing suppression of V1 responses and the perceptual consequences revealed via two-photon calcium imaging and transformer modeling

Continuous flash suppression (CFS), a dynamic masker presented to one eye suppressing the conscious perception of a stimulus shown to the other eye, has been extensively used to study visual consciousness. Various studies reported high-level visual and cognitive functions under CFS, which, however, has more recently been questioned and at least partially attributed to low-level stimulus properties. A key but unsettled issue is the extent to which the responses of V1 neurons, where inputs from two eyes first merge, are affected, as severely suppressed V1 responses would not sustain high-level processing. Here, we used two-photon calcium imaging to record the responses of large samples of V1 neurons to a grating stimulus under CFS in awake, fixating macaques. The results revealed that CFS substantially suppressed V1 orientation responses. Ocularity-wise, it nearly completely eliminated the orientation responses of V1 neurons preferring the masker eye or both eyes, while also significantly suppressing the responses of those preferring the grating eye. Modeling analyses suggest that, under CFS, the brain retains the ability of classifying coarse orientations, but may become less capable of reconstructing the grating stimulus. Consequently, while CFS-suppressed orientation information still supports low-level orientation discrimination, it may not suffice for high-level visual and cognitive processing.

neuroscience↗

bioRxiv2025

Human meibomian gland organoids to study epithelial homeostasis and dysfunction

Meibomian glands (MGs) are holocrine glands that secrete lipids to maintain the homeostasis of ocular surface, and their dysfunction leads to dry eye disease. Herein, we established long-term 3D organoid culture for murine and human MGs, which retained the cell lineages and lipid-producing ability. The organoids mimicked the drug treatment responses and generated functional MGs after orthotopic transplantation. Inspired by organoid cultures, we found FGF10 eye drops could rescue all-trans retinoic acid-induced MG dysfunction in mice. Besides, nicotinamide uniquely hampered the human MG organoid expansion by inhibiting FGF10 signaling. Single-cell atlas and lipidome not only aligned the delineated cell types and featured lipids between human MGs and organoids, but highlighting MAPK signaling inhibition enhanced acinar cell differentiation and functional maturation of MG organoids. In summary, this study established an organoid platform to explore epithelial homeostasis and dysfunction of MGs, facilitating drug development and regenerative medicine for dry eye disease.

cell biology↗