Biology subjects

Chen, X.

Publications and source records attributed to Chen, X..

At least 325 records · Page 18Linked to original sources

bioRxiv2025

Widespread transcriptional memory shapes heritable states and functional heterogeneity in cancer and stem cells

Recent studies show that non-genetic cellular heterogeneity, particularly through heritable cell states, fundamentally shapes cancer evolution and developmental trajectories. However, conventional single-cell transcriptomic snapshots lack temporal information needed to identify these heritable states. Here, we employ lineage-resolved single-cell transcriptomics to systematically map heritable cell states that persist across divisions, distinguishing them from transient fluctuations within a cell cycle. We uncover that heritable states are underpinned by widespread transcriptional memory, whereby gene expression is heritable, defining two classes of states in cancer and stem cells: clustered states, characterized by clustered gene expression, and latent states, marked by non-clustered gene expression. This memory shows unexpected conservation across cell types and conditions and is maintained by robust epigenetic mechanisms resistant to environmental perturbations. Functionally, memory genes predict critical behaviors including metastatic potential and lineage commitment, with latent-state genes often outperforming clustered-state genes. Our findings establish transcriptional memory as the molecular basis of heritable cellular heterogeneity, providing a framework for broadly understanding functional cellular variations across biological systems.

systems biology↗

bioRxiv2025

CanID: a robust and accurate RNAseq Expression-based diagnostic classification scheme for pediatric malignancies

Cancer subtype classification is critical for precision therapy and there is a growing trend of augmenting histopathology testing procedures with omics-based machine learning classifiers. However, analytical challenges remain for pediatric cancer on the scope and precision of the current classifiers as well as the evolving subtype standardization. To address these challenges, we built Cancer Identification or CanID, a stacked ensemble machine learning classification scheme, using the transcriptomic features derived from gene-level RNA sequencing count data as the sole input. CanID was developed primarily from 3203 pediatric cancer samples of 13 solid tumor subtypes and 38 hematologic malignancy subtypes with subtype labels curated without the use of RNA-seq data. The accuracies of independent testing in three independent or external data sets for Solid Tumor and Hematologic Malignancy are 99% and 92-93%, respectively. Notably, CanID was able to classify subtypes challenging for clinical histology evaluation and was robust to both biological and technical challenges, including differences in data collection protocols, class imbalance, potential mislabeled training samples and classes unobserved in training. The high accuracy, robustness, biological interpretability of this transcriptome-based classification scheme represents a valuable approach to advance tumor diagnosis and clinically meaningful stratification of tumor types. CanID can be accessed on GitHub at https://github.com/chenlab-sj/CanID.

bioinformatics↗

bioRxiv2025

Reelin Controls the Directional Orientation, Apical Localization and Length of Primary Cilia in Principal Neurons in the Cerebral Cortex

The primary cilia of pyramidal neurons in inside-out laminated regions orient predominantly toward the pia, reflecting reverse soma movement during postnatal neurodevelopment. However, the mechanisms underlying the directional cilia orientation are unknown. Here we show that the primary cilia of pyramidal neurons are localized near the base of the apical dendrites and aligned on the nuclear side opposite to the axon initial segment (AIS). However, this pattern is not observed in atypical pyramidal neurons in the deep neocortex, excitatory neurons in non-laminated regions, interneurons, or astrocytes, where cilia are irregularly positioned around the nuclei and lack preferred orientation. In Reelin-deficient mice (reeler), the directional orientation and apical location of cilia in late-born neocortical and CA1 neurons are disrupted. However, the initial impairments are partially corrected during postnatal development, along with a realignment of apical-basal orientation. In contrast, loss of Reelin drastically disrupts the directional orientation of cilia in early-born neocortical neurons and principal neurons in evolutionarily conserved cortical regions, which lack postnatal correction. Consistently, their cilia do not preferably localize to the apical side. Additionally, Reelin deficiency increases the cilia length of principal neurons across the cerebral cortex at a developmental stage when cilia stabilize in wild-type mice, but this effect is not observed in interneurons, astrocytes, or excitatory neurons in non-laminated regions. Together, Reelin controls the directional orientation, apical localization, and length of primary cilia in principal neurons in the cerebral cortex, underscoring the cilium as a key apical domain particularly prominent in late-born neurons.

neuroscience↗

bioRxiv2025

Arabidopsis Group I Pumilio RNA-binding factors are vital for embryo development and balancing between growth and stress resistance

Pumilio (PUM) RNA binding proteins are crucial for regulating gene expression by binding to a conserved motif in the 3'-untranslated region (3'-UTR). Despite their importance, the role of PUM in plants is largely unexplored. Here, we investigated the functions of Arabidopsis group I PUMs (APUM1-APUM6), which are ubiquitously expressed and localized in the cytosol. While single apum mutants exhibit no visible phenotypes, CRISPR/Cas9-generated apum1 apum2 apum3 triple mutants (apum1/2/3) display reduced growth in both vegetative and reproductive organs, alongside hypersensitivity to various stresses. Remarkably, apum1/2/3/4 quadruple mutants are embryonically lethal, highlighting their essential role in embryo development. Transcriptomic profiling revealed that differentially expressed genes (DEGs) upregulated in apum1/2/3 are enriched in pathways related to photosynthesis, stress responses and anthocyanin biosynthesis, while downregulated DEGs are associated with biotic stress defense and hydrogen peroxide metabolism. This suggests that APUM1/2/3 act as molecular hubs balancing plant growth and stress adaptation. Biochemical assays showed that recombinant APUM homologous domains bind to the 5-UGUGUAUA-3 core motif in the 3-UTR of the transcription factor Production of Anthocyanin Pigment1 (PAP1), crucial for anthocyanin biosynthesis. Notably, single nucleotide substitutions, except for the third U, do not affect binding, while multiple mutations disrupt interaction. Consistently, apum1/2/3 mutants accumulate significantly more anthocyanin than wild-type plants. Furthermore, we predicted 7053 potential target genes for APUM1/2/3, with 1609 present among the upregulated DEGs in apum1/2/3. Taken together, our findings demonstrate that group I APUMs are vital posttranscriptional regulators, providing a new perspective on the trade-offs between growth and stress resilience in plants.

plant biology↗

bioRxiv2025

Pyrimethamine inhibits mutant NRF2 as a molecular glue

Esophageal squamous cell carcinoma (ESCC) is a deadly disease and one of the most aggressive cancers of the gastrointestinal tract. As a master transcription factor regulating the stress response, nuclear factor erythroid 2-related factor 2 (NRF2) is often mutated, loses negative regulation by Kelch-like ECH-associated protein 1 (KEAP1), becomes hyperactive, and thus causes chemo-radioresistance and poor survival in human ESCC. Our previous research identified pyrimethamine (PYR) as an NRF2 inhibitor and demonstrated that inhibition of dihydrofolate reductase (DHFR) is the major mechanism of its action. Based on these findings, PYR has advanced into a Phase I window-of-opportunity clinical trial. In this study, using isogenic ESCC cell lines, we aimed to investigate the phenotypic consequences of NRF2 activation in ESCC cells and further elucidate the mechanism of action of PYR. While overexpression of wild-type NRF2 (NRF2WT) promoted squamous differentiation and suppressed proliferation, expression of mutant NRF2 (NRF2Mut) produced mixed effects on differentiation markers and promoted proliferation. NRF2 activation reduced sensitivity to chemotherapy and radiation, whereas PYR treatment restored chemosensitivity and radiosensitivity in NRF2Mut ESCC cells. Co-immunoprecipitation and proximity ligation assays revealed that PYR selectively enhanced the interaction between NRF2W24C and KEAP1, but not between NRF2WT and KEAP1. Isothermal titration calorimetry (ITC) confirmed the direct binding of PYR to KEAP1 and surface plasmon resonance (SPR) showed that PYR modestly facilitated the interaction between a DLGW24C peptide and the Kelch fragment. Molecular docking suggested that PYR bound to a pocket within the Kelch domain near Arg415. In summary, NRF2 activation promotes cell proliferation and therapy resistance in ESCC in a context-dependent manner. PYR functions as a modest molecular glue that selectively restores KEAP1 binding to NRF2W24C, providing a potential therapeutic strategy for NRF2Mut ESCC.

cancer biology↗

bioRxiv2025

Epilepsy-Associated SCN2A-L1342P Mutation Drives Network Hyperexcitability and Widespread Transcriptomic Changes in Human Cortical Organoids

ObjectiveSCN2A pathogenic mutations, such as the recurrent heterozygous Nav1.2-L1342P, are monogenic causes of epilepsy. In this human-induced pluripotent stem cell model system, we aim to investigate the molecular and cellular mechanisms underlying the SCN2A-L1342P-associated pathology. MethodsUsing a human male iPSC reference line (KOLF) carrying the Nav1.2-L1342P mutation, we generated 3D cortical organoids for functional studies. Patch clamp and multi-electrode array (MEA) recordings, immunocytochemistry, and RNA sequencing were used to characterize the disease phenotypes. ResultsNav1.2-L1342P organoid neurons displayed increased intrinsic excitability, and amplified excitatory post-synaptic currents, which are consistent with an increase in excitatory synapse formation revealed by PSD95/SYN1 immunostaining. Moreover, elevated network firing activity, as demonstrated by MEA, indicates a pronounced network hyperexcitability. Transcriptomic profiling of organoids carrying the Nav1.2-L1342P mutation further revealed significant alterations in synaptic, glutamatergic, and developmental pathways. SignificanceOur findings demonstrate that the Nav1.2-L1342P mutation drives a multifaceted disease phenotype, including network hyperexcitability and disruption of pathways related to neuronal and synaptic functions. These results advance our understanding of SCN2A-related Developmental and Epileptic Encephalopathy (DEE), laying a foundation for personalized interventions. Key PointsO_LIKey Point 1: Human neurons carrying epilepsy-causing SCN2A-L1342P display intrinsic hyperexcitability in cortical organoids. C_LIO_LIKey Point 2: Synaptic transmission is enhanced in organoids carrying the SCN2A-L1324P mutation, consistent with the presence of elevated excitatory synapses, which leads to increased network hyperexcitability. C_LIO_LIKey Point 3: Transcriptomics analysis reveals that the SCN2A-L1342P mutation causes significant differential changes in forebrain developmental genes, synaptic and glutamatergic signaling pathways, and enhances cellular senescence and apoptosis. C_LI

neuroscience↗

bioRxiv2025

Active regulation of the epidermal growth factor receptor by the membrane bilayer

Cell surface receptors transmit information across the plasma membrane to connect the extracellular environment to intracellular function. While the structures and interactions of the receptors have been long established as mediators of signaling, increasing evidence suggests that the membrane itself plays an active role in both suppressing and enhancing signaling. Identifying and investigating this contribution has been challenging owing to the complex composition of the plasma membrane. We used cell-free expression to incorporate the epidermal growth factor receptor (EGFR) into nanodiscs with defined membrane compositions and characterized ligand-induced transmembrane conformational response and interactions with signaling partners using single-molecule and ensemble fluorescence assays. We observed that both the transmembrane conformational response and interactions with signaling partners are strongly lipid dependent, consistent with previous observations of electrostatic interactions between the anionic lipids and conserved basic residues near the membrane adjacent domain. Strikingly, the active conformation of EGFR and high levels of ATP binding were maintained regardless of ligand binding with high anionic lipid content typical of cancer cells, where EGFR signaling is enhanced. In contrast, the conformational response was suppressed in the presence of cholesterol, providing a mechanism for its known inhibitory effect on EGFR signaling. Our findings introduce a model of EGFR signaling in which the lipid environment can override ligand control, providing a biophysical basis for both robust EGFR activity in healthy cells and aberrant activity under pathological conditions. The membrane-adjacent protein sequence, likely responsible for the lipid dependence, is conserved among receptor tyrosine kinases, suggesting that active regulation by the plasma membrane may be a general feature of this important class of proteins.

biophysics↗

bioRxiv2025

PXDesign: Fast, Modular, and Accurate De Novo Design of Protein Binders

PXDesign achieves nanomolar binder hit rates of 17-82% across six of seven diverse protein targets, surpassing prior methods such as AlphaProteo. This experimental success rate is enabled by advances in both binder generation and filtering. We develop both a diffusion-based generative model (PXDesign-d) and a hallucination-based approach (PXDesign-h), each showing strong in silico performance that outperforms existing models. Beyond generation, we systematically analyze confidence-based filtering and ranking strategies from multiple structure predictors, comparing their accuracy, efficiency, and complementarity on datasets spanning de novo binders and mutagenesis. Finally, we validate the full design process experimentally, achieving high hit rates and multiple nanomolar binders. To support future research and broaden community adoption, we release the full PXDesign pipeline (https://github.com/bytedance/PXDesign), provide public access to PXDesign through a dedicated web server (https://protenix-server.com), and make all designed binder sequences available at the project page (https://protenix.github.io/pxdesign). O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=75 SRC="FIGDIR/small/670450v3_ufig1.gif" ALT="Figure 1"> View larger version (25K): org.highwire.dtl.DTLVardef@2a414aorg.highwire.dtl.DTLVardef@248f85org.highwire.dtl.DTLVardef@4a6afdorg.highwire.dtl.DTLVardef@1b622dd_HPS_FORMAT_FIGEXP M_FIG C_FIG

molecular biology↗

bioRxiv2025

Functional recovery by transplantation of human iPSC-derived A2B5 positive neural progenitor cell after spinal cord injury in mice

Human induced pluripotent stem cells (hiPSCs) hold great potential for patient-specific therapies. Transplantation of hiPSC-derived neural progenitor cells (NPCs) is a promising reparative strategy for spinal cord injury (SCI), but clinical translation requires efficient differentiation into desired neural lineages and purification before transplantation. Here, differentiated hiPSCs--reprogrammed from human skin fibroblasts using Sendai virus-mediated expression of OCT4, SOX2, KLF4, and C-MYC--into neural rosettes expressing SOX1 and PAX6, followed by neuronal precursors ({beta}-tubulin III/NESTIN) and glial precursors (GFAP/NESTIN). Both neuronal and glial precursors expressed the A2B5 surface antigen. A2B5+ NPCs, purified by fluorescence-activated cell sorting (FACS), proliferated in vitro with mitogens and differentiated into mature neurons and astrocytes under lineage-specific conditions. NOD-SCID mice received a T9 contusion injury followed by transplantation of A2B5+ NPCs, human fibroblasts, or control medium at 8 days post-injury. At two months, grafted NPCs showed robust survival, progressive neuronal maturation ({beta}-tubulin III [->] doublecortin [->] NeuN), and astrocytic differentiation (GFAP), particularly in spared white matter. Transplantation significantly increased spared white matter volume and improved hindlimb locomotor recovery, with no teratoma formation observed. These results demonstrate that hiPSC-derived, FACS-purified A2B5+ NPCs can survive, differentiate into neurons and astrocytes, and enhance functional recovery after SCI. This approach offers a safe and effective candidate cell source for treating SCI and potentially other neurological disorders.

neuroscience↗

bioRxiv2025

DeepHalo: Deep Learning-Powered Exploration of Halogenated Metabolites Uncovering Antibacterial Depsipeptides

In the omics era, confident high-throughput analytical tools are crucial for the efficient identification of metabolites. Here, we present DeepHalo, a deep learning-integrated and hierarchically optimized workflow designed for high-throughput exploration of halogenated metabolites from high-resolution mass spectrometry-based metabolomics. DeepHalo leverages deep learning models combined with a comprehensive scoring to enhance the reliability of halogen predictions. It integrates PyOpenMS for fast isotope pattern detection and incorporates a halogen-based dereplication algorithm with GNPS molecular networking to efficiently exploit and annotate halogenates from complex biological matrices. To validate its performance, DeepHalo was applied to explore halogenated metabolites from 1,296 microbial culture crude, leading to the discovery of six families of structurally diverse halogenated molecules. This included a new class of cyclic depsipeptides, aglomycins A-E, featuring rare 3-chloroanthranilic acid and/or epoxyvaline blocks. Additionally, a plausible biosynthetic pathway of aglomycins was proposed through bioinformatics analyses and targeted gene knockout experiments. Bioassays revealed that aglomycin A exhibits synergistic antibacterial activity with linezolid against vancomycin-resistant Enterococcus faecium (VRE) both in vitro and in vivo. We envision that DeepHalo (freely available at https://github.com/xieyying/DeepHalo) will become a powerful tool for accelerating the discovery of halogenated "dark matter".

biochemistry↗

bioRxiv2025

Betrixaban Activates cGAS and ERVs to Promote Dual Nucleic-Sensing Antiviral Immunity

Broad-spectrum host-directed antivirals are urgently needed, as virus-targeted drugs often suffer from narrow specificity and rapid resistance. Here, we reported that Betrixaban (BT), an FDA-approved oral Factor Xa inhibitor, induced a robust antiviral state through dual innate immune pathways. Mechanistically, we identified BT directly bound and activated the DNA sensor cGAS to induce cGAMP production, representing BT as the first small-molecule cGAS agonist. Concurrently, BT inhibited histone deacetylases (HDACs), leading to chromatin de-repression of endogenous retroviruses (ERVs) and production of immunostimulatory double-stranded RNA (dsRNA) that engaged RIG-I/MDA5. These combined signal cascades triggered strong type I interferon responses and conferred broad-spectrum antiviral protection against RNA and DNA viruses in vitro and in vivo. These findings unveil a unique host-directed antiviral strategy wherein a small molecule drug engage dual nucleic acid-sensing pathway, and suggest repurposing BT as an orally broad-spectrum antiviral. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=190 SRC="FIGDIR/small/669242v1_ufig1.gif" ALT="Figure 1"> View larger version (68K): org.highwire.dtl.DTLVardef@aa153dorg.highwire.dtl.DTLVardef@585d43org.highwire.dtl.DTLVardef@152ec59org.highwire.dtl.DTLVardef@11ada33_HPS_FORMAT_FIGEXP M_FIG C_FIG

immunology↗

bioRxiv2025

Unveiling the Role of PHF20 in TBC1D4-Mediated Glucose Uptake During Toxoplasma gondii Infection

BackgroundToxoplasma gondii relies on host cell nutrients, especially glucose, to support its intracellular growth. However, the mechanisms by which it enhances host glucose metabolism remain incompletely understood. MethodsWe used fluorescence-based glucose uptake assays, flow cytometry, metabolic flux analysis, and gene silencing in ARPE-19 cells, along with transgenic mouse models, to explore how T. gondii manipulates host glucose utilization and whether this promotes parasite proliferation. ResultsT. gondii infection significantly enhanced host glucose uptake in a dose-dependent manner and promoted GLUT4 translocation to the plasma membrane. Notably, extracellular acidification rate (ECAR) assays demonstrated a marked increase in glycolytic activity following infection. Mechanistically, we identified that the PI3K/AKT signaling pathway mediates the phosphorylation and transcriptional upregulation of TBC1D4, a Rab-GAP protein essential for GLUT4 trafficking. Genetic silencing of TBC1D4 impaired both glucose uptake and parasite replication. Furthermore, we uncovered a regulatory mechanism involving AKT-dependent nuclear signaling that modulates TBC1D4 transcription. In vivo experiments using Phf20 transgenic mice confirmed increased susceptibility to T. gondii and elevated glucose metabolic responses. ConclusionsOur study reveals that T. gondii hijacks a host PI3K/AKT-TBC1D4 axis to enhance glucose uptake and glycolysis, thereby ensuring metabolic support for its proliferation. These findings highlight host glucose metabolism as a potential therapeutic target for controlling toxoplasmosis.

cell biology↗

bioRxiv2025

A Core Pattern of Cerebellar and Brainstem Degeneration and Reduced Cerebrocerebellar Structural Covariance in Spinocerebellar Ataxia Type 3 (SCA3): MRI Volumetrics from ENIGMA-Ataxia

ObjectiveSpinocerebellar ataxia type 3 (SCA3) is a rare, inherited neurodegenerative disease. Here, we profile the spatial spread of atrophy across the whole brain, determine whether brain degeneration preferentially maps onto specific functional networks, and investigate the relationship between cerebellar and cerebral anatomical changes. MethodsWhole-brain grey and white matter (GM and WM) voxel-based morphometry was performed on 408 individuals with SCA3 (82 pre-ataxic) and 293 controls. The SCA3 cohort was stratified by ataxia severity to investigate disease progression, with cerebellar GM atrophy mapped onto a task-based functional atlas. Volume was correlated with disease duration and intensity. Cerebrocerebellar volumetric covariance was assessed to determine whether atrophy was coupled between infra- and supratentorial regions. ResultsThe pattern of atrophy is spatially consistent but progressive in magnitude across the disease course. The greatest atrophy was found in the pons, cerebellar WM, and cerebellar peduncles; correlations with disease severity and duration were also strongest in these regions. Cerebellar GM atrophy was greatest in functional regions associated with motor execution and planning, attention, and emotional processing. Sparse cerebral cortical atrophy appears only in the most severe disease subgroup, while striatal atrophy begins in the earliest stages. Reduced cerebrocerebellar structural covariance is observed in SCA3 participants versus controls. InterpretationWhile cerebellar and brainstem atrophy become more severe, the pattern of atrophy remains largely consistent as SCA3 progresses. Cerebellar GM degeneration occurs in regions associated with motor, cognitive, and affective control, in line with clinical presentation. Cerebellar atrophy is not directly mirrored by cerebral changes.

neuroscience↗

bioRxiv2025

Genomic footprints of domestication in almond (Prunus dulcis)

The domestication of perennial crops in the Mediterranean Basin remains unclear, particularly regarding the genomic consequences of human-mediated demographic shifts and selection. We analyzed 8.1 million single nucleotide polymorphisms from 96 cultivated almond (Prunus dulcis) accessions from Europe, North America, Central Asia, and New Zealand, alongside four wild relatives. Population structure analyses revealed four geographically differentiated cultivated groups (Central Asian, North American, and two European) and three wild populations (P. spinosissima, P. orientalis, and P. fenzliana). Cultivated almonds retained high genetic diversity, consistent with weak domestication bottlenecks typical of outcrossing perennials. Elevated diversity and private allele counts in Central Asian cultivars, with limited gene flow, support this region as an independent cradle of domestication. In contrast, extensive wild-to-crop gene flow--especially involving P. orientalis--has shaped the genomes of European and North American almonds. Genome-wide scans for selective sweeps showed most candidate genes under selection were population-specific, though often associated with similar biological functions, including stress responses and agronomic traits. This suggests repeated targeting of comparable pathways during domestication, despite distinct selection histories. Several selected genes in cultivated populations overlapped with those in wild relatives, particularly P. orientalis. Combined with demographic inferences indicating wild populations persistence through past climate fluctuations, these findings suggest wild gene pools retain adaptive alleles--either ancestrally shared or introgressed--that contributed to cultivated diversity. Altogether, our results reveal a complex, multi-regional domestication history for almonds, shaped by gene flow and recurrent selection. This study emphasizes wild relatives as adaptive diversity sources and reveals genomic bases of perennial crop evolution.

genomics↗

bioRxiv2025

Tumor necrosis factor receptor 2 inhibits HIV-1 infection by blocking the binding of gp120 to CD4

The HIV-1 envelope glycoprotein gp120 binds to CD4 molecule and then undergoes conformational changes to interact with the co-receptors CCR5 or CXCR4, resulting in cellular entrance. However, certain types of cells, such as macrophages and CD4+Foxp3+ regulatory T cells (Tregs), have shown to resist HIV-1 infection despite co-expressing CD4 and co-receptors. In this study, we found that TNF receptor type II (TNFR2) directly bound to gp120, with the binding site on gp120 in close proximity to that of CD4. Intriguingly, exogenous TNFR2 had the capacity to inhibit the binding of gp120 to CD4 T cells. Furthermore, the infection of CD4+CCR5+ cells by pseudoviruses containing the HIV-1 envelope was inhibited by TNFR2 protein. In contrast, TNFR1, similar in structure to TNFR2 and sharing the same ligand, failed to inhibit the infection of CD4+ T cells by HIV-1 pseudoviruses. This property of TNFR2 may be harnessed in the prevention or treatment of HIV-1 infection and thus warrant future investigation. SUMMARYThis study reveals that TNFR2 directly binds to HIV-1 gp120, inhibiting its interaction with CD4 and reducing HIV-1 infection in CD4+ T cells. The findings highlight TNFR2s potential role in protecting cells and offer insights for HIV-1 prevention or therapy.

immunology↗

bioRxiv2025

Hi-Cformer enables multi-scale chromatin contact map modeling for single-cell Hi-C data analysis

Single-cell Hi-C captures the three-dimensional organization of chromatin in individual cells and provides insights into fundamental genomic processes such as gene regulation and transcription. While analyses of bulk Hi-C data have revealed multi-scale chromatin structures like A/B compartments and topologically associating domains, single-cell Hi-C data remain challenging to analyze due to sparsity and uneven distribution of chromatin contacts across genomic distances. These characteristics lead to strong signals near the diagonal and complex multi-scale local patterns in single-cell contact maps. Here, we propose Hi-Cformer, a transformer-based method that simultaneously models multi-scale blocks of chromatin contact maps and incorporates a specially designed attention mechanism to capture the dependencies between chromatin interactions across genomic regions and scales, enabling the integration of both global and fine-grained chromatin interaction features. Building on this architecture, Hi-Cformer robustly derives low-dimensional representations of cells from single-cell Hi-C data, achieving clearer separation of cell types compared to existing methods. Hi-Cformer can also accurately impute chromatin interaction signals associated with cellular heterogeneity, including 3D genome features such as topologically associating domain-like boundaries and A/B compartments. Furthermore, by leveraging its learned embeddings, Hi-Cformer can be extended to cell type annotation, achieving high accuracy and robustness across both intra- and inter-dataset scenarios.

bioinformatics↗

bioRxiv2025

Population genomics of the endangered scaly-foot snail defines conservation units amid deep-sea mining threats in Indian Ocean vents

Hydrothermal vents in the Indian Ocean face imminent deep-sea mining, yet lack baseline high-resolution connectivity data for their endemic fauna. We present the first population genomic study of the endangered scaly-foot snail (Chrysomallon squamiferum), an iconic species distributed across three vent biogeographic provinces. Analysing 125 individuals from eight vent fields using 14 million single-nucleotide polymorphisms, we identify five genetic groups that warrant recognition as evolutionarily significant units. Demographic modelling reveals critical contributions from extinct or unsampled phantom populations to the contemporary genetic structure. Together with physical ocean modelling, we show that the deep currents drive asymmetric south-to-north gene flows, while transform faults act as dispersal barriers. We propose Longqi-Duanqiao fields on the Southwest Indian Ridge and Wocan field on the Carlsberg Ridge as two isolated populations prioritised for protection. Given its exceptional adaptations, wide distribution, and public recognition, the scaly-foot snail is well-positioned to serve as both a flagship and umbrella species to ensure the survival of a broader suite of vent biodiversity. As the International Seabed Authority finalises its Mining Code in 2025, our findings provide essential genomic evidence to mitigate the impacts of mining on genetic diversity and inform transboundary conservation strategies for this vulnerable ecosystem.

ecology↗

bioRxiv2025

Structures of dynamic interactors at native proteasomes by PhIX-MS and cryoelectron microscopy

Proteasome function depends on a network of transient interactions that remain structurally and functionally unresolved. We developed PhIX-MS (Photo-induced In situ Crosslinking-Mass Spectrometry), a structural proteomics workflow that stabilizes transient interactions in cells by UV-activated crosslinking to capture topological information. Applying PhIX-MS with cryo-electron microscopy (cryo-EM), we mapped redox sensor TXNL1 at the proteasome regulatory particle (RP), placing its PITH domain above deubiquitinase RPN11 and resolving its dynamic thioredoxin domain near RPN2/PSMD1 and RPN13/ADRM1, ideally located to reduce substrates prior to proteolysis. We also resolved chaperone PSMD5 bound to RP without the proteolytic core particle (CP) where its C-terminus inserts into the ATPase pore blocking CP binding. PhIX-MS and AlphaFold modeling tether ubiquitin ligase UBE3C/Hul5 along the RP placing its catalytic site above the RPN11 active site, enabling their coupled activities. Our integrative approach enables the localization of native, low-affinity protein interactions and is broadly applicable to dynamic macromolecular assemblies.

cell biology↗