Biology subjects

Hong, J.

Publications and source records attributed to Hong, J..

At least 19 recordsLinked to original sources

bioRxiv2026

m6A-Driven Intratumoral Cholesterol Biosynthesis Fuels Castration-Resistant Prostate Cancer Progression

Both nuclear pore complexes (NPCs) and RNA N6-methyladenosine (m6A) machinery are indispensable for proper cellular function. Although their collaborative roles in the nuclear export of messenger RNAs (mRNAs) have been reported, it remains ambiguous whether and how this collaboration may contribute to cancer progression. Here we identify a functional cooperation between NPCs and m6A signaling that promotes the development of castration-resistant prostate cancer (CRPC). We showed that nuclear export of m6A-modified mRNAs, mediated by the interaction between RNA methyltransferase METTL3 and the nucleoporin NUP93, is functionally coupled to cholesterol biosynthesis. Given that cholesterol-fueled intratumoral androgen production is one of the mechanisms driving CRPC, we demonstrated that overexpression of the wild-type METTL3 or NUP93, but neither the enzymatically dead METTL3 nor the mutant NUP93 that loses METTL3-interacting capability, elevates intracellular levels of androgens, activates AR signaling under castrate condition, and promotes androgen-independent growth of prostate cancer cells both in vitro and in vivo. Importantly, pharmacological inhibition of METTL3 or targeted demethylation on mRNAs encoding key cholesterol biosynthesis enzymes effectively suppressed CRPC malignancy. Together, these findings uncover a therapeutically targetable m6A-METTL3-NUP93 axis that links nuclear mRNA export and metabolic reprogramming to fuel CRPC progression, providing a conceptually new strategy for the treatment of this lethal disease.

cancer biology↗

bioRxiv2026

Parental Genome Assemblies of Suyunuo1 Reveal Structural Variation Underlying Edible Waxy Maize Evolution, Superior Hybrid Performance and Yield - Flavor Balance

Edible waxy maize is a unique domesticated cereal valued for its superior sensory and nutritional properties, yet high quality gap free genomes remain lacking, hindering the exploration of structural variations (SVs) and domestication related divergence. Here, we assembled two chromosome level, gap free genomes of the elite waxy maize inbred lines Tongxi 5 and Hengbai 522, the parents of the widely cultivated hybrid Suyunuo 1. Comparative genomic analysis revealed substantial genome size variation, prominent megabase scale SVs, and extensive knob repeat expansion in Tongxi 5. We identified widespread gene presence absence variation and hyperdivergent regions enriched in transposable elements, which largely underpin genomic differentiation between waxy and field maize. Population genomic analyses further demonstrated asymmetric introgression from field maize into the two parents, whereas the conserved waxy haplotype supports a shared ancestral origin. Integrative GWAS based on SNPs, InDels and SVs revealed that SVs substantially contribute to phenotypic diversity and mediate the co-regulation of yield traits and flavor-related metabolites. Our results uncover key genomic events underlying post-domestication divergence and highlight the essential roles of SVs in heterosis and flavor-yield balance, providing valuable genomic resources for waxy maize improvement.

plant biology↗

bioRxiv2026

Common viral infections seed regionally distinct resident memory T cells in the human CNS

T cells persist in the central nervous system (CNS) and can drive both protection and neurological disease. How these cells are organized in humans and what they recognize is largely unknown. Here, we profiled CD8 T cells across anatomically distinct CNS regions, obtained through on-site autopsies and temporal lobe resection surgeries, using single-cell RNA sequencing, paired T cell receptor sequencing, and DNA-barcoded tetramers. Resident memory T cells (TRM) specific for Epstein-Barr virus, cytomegalovirus, influenza A, and SARS-CoV-2 were identified across CNS compartments. Anatomical location was the strongest correlate of TRM cell state, with leptomeningeal cells adopting a cytokine-poised TRM program, whereas brain TRM cells were transcriptionally restrained. Cells of the same clonotype spanned tissues yet adopted local transcriptional states. Viral specificity added another layer of TRM heterogeneity with GZMK/GZMA-expressing EBV-specific populations and interferon-stimulated gene signatures in SARS-CoV-2 and Influenza A-specific cells. The human CNS thus harbors regionally distinct CD8+ TRM shaped by common viral exposures.

immunology↗

bioRxiv2026

Dual-targeted nanoparticles enable the ex vivo generation of cytotoxic and phagocytic CAR effector cells

Chimeric antigen receptor (CAR)-T cells and CAR-macrophages (or CAR-monocytes) offer complementary antitumor functions. CAR-T cells exert potent cytotoxicity against cancer cells, whereas CAR-macrophages can infiltrate solid tumors, phagocytose cancer cells and promote antigen spreading. Antibody-conjugated lipid nanoparticles (LNPs) have emerged as non-viral mRNA delivery platforms for generating CAR-immune cells. However, these systems have generally been optimized to target a single immune-cell type. Here, to enable the ex vivo generation of CAR-T cells and CAR-monocytes, we developed CLCM08, an anti-CD222 antibody, and co-displayed it with an anti-CD5 antibody on LNPs. CD222 is predominantly expressed by monocytes, macrophages and T cells, and facilitates the internalization of CD222-binding molecules. CD5 is primarily expressed by T cells and has previously been used to enable LNP-mediated mRNA delivery to these cells. Delivery of CAR mRNA by dual CD222/CD5 antibody-conjugated LNPs to primary monocytes and T cells substantially enhanced the ex vivo generation of CAR-monocytes and CAR-T cells compared with non-conjugated LNPs. Moreover, CD19 CAR-T cells and CAR-monocytes generated using dual CD222/CD5 antibody-conjugated LNPs showed enhanced cytotoxic and phagocytic activity, respectively, relative to cells generated using non-conjugated LNPs, with anti-CD222 LNPs producing the largest phagocytic gain in monocytes. These findings establish an adaptable antibody-conjugated LNP-mRNA platform for the ex vivo generation of CAR-T cells and CAR-monocytes.

biochemistry↗

bioRxiv2026

Dynamics and geometry of emotion and cognition: an interpretable model of individual human behavior

Affective flexibility-the capacity to flexibly process emotional information-has been assessed with affective task switching, in which response times consistently reveal larger behavioral costs when switching to the affective task. These traditional metrics of task behavior, however, discard the sub-trial dynamics that produce them and are vulnerable to trial-sampling noise. Subject-specific generative models were independently fitted (22 adults) with response-time sequences. The learned dynamics were visualized as continuous trajectories in a labeled embedding that was shared across person-specific models, yielding a suite of interpretable geometric metrics that captured how sub-trial behavior is jointly shaped by experimental conditions and between-subject variability. Switch-repeat onset distance tracked individual differences in switch costs; early- and late-epoch tortuosity provided convergence with classical sub-process models; and angular alignment between trajectories supported a task set flexibility account of asymmetric switch costs. Overall, our approach demonstrates the utility of latent geometry for deriving mechanistically informative measures of individual task behavior.

neuroscience↗

bioRxiv2026

Balancing spatial resolution and proteome depth in LC-MS based spatialproteomics

Spatial proteomics aims to resolve protein composition within intact tissues, yet extraction-based liquid chromatography-mass spectrometry (LC-MS) workflows face an inherent trade-off: smaller sampling units increase spatial specificity, whereas larger sampling units provide greater proteome depth and robustness. As analytical sensitivity improves, sampling-unit size therefore becomes a key experimental design parameter. Current extraction-based LC-MS workflows typically rely on laser capture microdissection (LCM), where sample recovery and scalability can become limiting at low input. Spatially resolved laser-activated cell sorting (SLACS) offers an alternative tissue-isolation strategy based on single-pulse near-infrared laser activation. Here, we use SLACS to systematically examine the resolution-sensitivity trade-off across sampling units ranging from single-cell-equivalent to larger low-input tissue regions. Few-cell sampling retained substantial proteomic information relative to larger regions while increasing spatial specificity. Applied to the mouse somatosensory cortex, SLACS generated deep, layer-resolved proteomic profiles from regions corresponding to approximately 60 cells and preserved major layer-specific molecular patterns at inputs as low as approximately 6 cells. These results highlight sampling-unit size as an important experimental design parameter in extraction-based spatial proteomics and support few-cell sampling as a practical compromise between spatial specificity, proteome depth and robustness.

biochemistry↗

bioRxiv2026

The KRAS G12C Inhibitor Divarasib Stabilizes RBM39 and Antagonizes Aryl-Sulfonamide Degraders

KRAS G12C inhibitors have demonstrated meaningful clinical benefit in KRAS G12C-mutant non-small cell lung cancer (NSCLC), yet responses remain heterogeneous and treatment-associated toxicities persist for reasons that are incompletely understood. Cysteine profiling indicates that these covalent inhibitors are highly selective for mutant KRAS; however, such approaches cannot detect noncovalent engagement of additional non-RAS proteins. Here, we used a protein-folding stability profiling technique, stability of proteins from rates of oxidation (SPROX), to identify protein targets of the clinical KRAS G12C inhibitor, divarasib (GDC-6036), in KRAS-mutant NSCLC lysates. SPROX revealed a focused set of candidate interactors, including the essential splicing factor RBM39, which was reproducibly stabilized at both divarasib concentrations tested. We subsequently confirmed that divarasib directly and noncovalently binds to RBM39 protein. In NSCLC cells, divarasib increased RBM39 protein abundance and antagonized RBM39 degradation induced by the aryl-sulfonamide molecular glue indisulam through a post-transcriptional mechanism. Divarasib and RBM39 degraders reciprocally antagonized each other's cytotoxicity, and RBM39 knockdown modestly reduced divarasib-induced cell death. Mechanistically, divarasib-mediated RBM39 stabilization regulated both INSR expression and alternative splicing, altered downstream insulin receptor signaling, and contributed to divarasib-associated cytotoxicity. Consistent with these findings, RBM39 and INSR expression were positively correlated across multiple human cancer types. Collectively, these findings identify RBM39 as a previously unrecognized noncovalent target of divarasib and uncover an RBM39-INSR signaling axis that modulates cellular responses to both divarasib and RBM39 degraders.

pharmacology and toxicology↗

bioRxiv2026

FABP8/PMP2 is a positive regulator of PNS myelination

Myelin formation in peripheral nerves is orchestrated by axon-derived signals and the ability of Schwann cells to expand lipid-rich membrane. Axonal Neuregulin-1 type III (NRG1t3) is known to promote thicker myelin and is associated with increased lipid abundance in peripheral nerves. NRG1t3 also strongly upregulates peripheral myelin protein 2 (FABP8/PMP2), a fatty acid binding protein in myelinating Schwann cells. Here, we directly tested whether elevating PMP2 in Schwann cells is sufficient to enhance myelin growth in nerves. We generated transgenic mice with Schwann cell-specific PMP2 overexpression and showed that PMP2 overexpression drove significant myelin thickening in peripheral nerves, without altering myelin ultrastructure, impairing nerve conduction, or causing detectable adverse effects despite sustained expression. Strikingly, this hypermyelination occurred without activating canonical promyelinating signaling pathways. Instead, elevated PMP2 selectively enhanced fatty acid uptake in Schwann cells, identifying PMP2 as a dosage sensitive enhancer of myelin growth. These findings suggest that in the absence of axonal signaling-driven upregulation, enhanced PMP2 expression itself promotes myelin membrane expansion and enhanced fatty acid availability that could favor complex lipid synthesis. These findings reveal new role for PMP2 as a regulator for myelin expansion in vivo, highlighting a key link between lipid trafficking and myelin growth.

neuroscience↗

bioRxiv2026

Staged heavy-chain filtering enables Fab discovery from combinatorially intractable library spaces

BackgroundCombinatorial fragment antigen-binding (Fab) libraries encode an immense heavy-light chain pairing space, often exceeding 10{superscript 1} possible combinations, which far surpasses the diversity that can be experimentally constructed and screened in display systems. As a result, direct Fab screening samples only a small fraction of the theoretical search space, creating a practical bottleneck for functional binder discovery. ResultsHere, we frame Fab discovery as a staged search problem by decoupling heavy-chain (HC) and light-chain (LC) exploration. We implemented a sequential HC preselection-remating workflow in yeast surface display, in which antigen-reactive HC variants are first enriched and subsequently recombined with a diverse LC repertoire to reconstruct a focused Fab library. In a SARS-CoV-2 spike-targeted campaign, HC and LC libraries of 2.05 x 10 and 2.33 x 10 members corresponded to a theoretical pairing space of approximately 4.8 x 10{superscript 1} combinations. Sequential HC enrichment followed by LC remating allowed recovery of multiple functional Fab clones from a tractable library scale of approximately 10, including clones that shared a common HC scaffold but carried distinct LC partners. A representative recombinant IgG output showed broad but heterogeneous spike/RBD binding, measurable pseudovirus neutralization activity (EC = 11.1 nM), and compatibility with standard early biophysical characterization after full-length IgG reformatting. ConclusionsThese results provide proof of principle that combinatorial Fab discovery can be approached as a staged exploration problem under realistic library-size constraints. By focusing downstream Fab reconstruction on an antigen-compatible HC subspace, sequential HC preselection followed by LC remating offers a practical strategy for exploring otherwise intractable antibody pairing landscapes in eukaryotic display systems.

bioengineering↗

bioRxiv2026

Hepatocellular Carcinoma Revisited from Single Cell Sequencing: Dynamic Evolution from Epithelial Dedifferentiation to Mesenchymal Remodeling

BackgroundSingle-cell RNA sequencing has provided new insights into hepatocellular carcinoma (HCC); however, a unified understanding of epithelial heterogeneity and immune evasion strategies in HCC remains lacking. MethodsWe re-analyzed publicly available single-cell datasets using conventional bioinformatics pipelines. Cell-type annotation of epithelial and T cell populations was further validated across multiple independent datasets to ensure robustness. ResultsWe systematically examined epithelial, immune, myeloid, and stromal lineages. In addition to recapitulating previously reported findings, we identified several novel observations. Notably, we uncovered a three-step dedifferentiation trajectory in epithelial cells and confirmed a bidirectional differentiation pattern within CD8{square} T cells. We also identified a subset of GZMK{square} CD4{square} T cells, whose transcriptional features resemble but are distinct from T follicular helper (Tfh) cells. Importantly, transcriptional drift within myeloid populations appeared to be closely associated with immune responsiveness. Furthermore, ligand-receptor analysis highlighted a potential cooperative role of LAMP3{square} dendritic cells and Tfh cells in promoting lymphoid follicle formation. ConclusionsIn the era of rapidly evolving single-cell sequencing technologies, we provide a framework for understanding cellular heterogeneity in HCC, which awaits further validation in future studies.

cancer biology↗

bioRxiv2026

Subunit selective modulation of GABAA receptors using pharmacogenetically tethered neurosteroids

Neurosteroids are powerful endogenous modulators of inhibition and emerging therapeutics for anxiety, epilepsy, and mood disorders, yet their actions at defined receptor subtypes and within specific neuronal populations remain poorly resolved. Here, we engineer a neurosteroid DART (Drug Acutely Restricted by Tethering) platform to deliver neuroactive steroid (NAS) activity with cellular precision and receptor-subunit selectivity. From a screen of seventeen NAS analogs, we identified seven scaffolds suitable for further engineering, and we discovered that linker attachment at the steroid C11 position uniquely preserves NAS positive allosteric modulation of GABAA receptors, whereas C2 and C17 attachment abolished activity. C11-linked NAS-DARTs slowed IPSC decay kinetics and showed variable off-target modulation of NMDA and AMPA EPSCs. The lead DART compound, YX85.1DART.2, enhanced GABA-evoked currents in neurons expressing engineered 4/{delta}-containing GABAA receptors but spared {gamma}2-containing receptors. A complementary benzodiazepine DART BZP.1DART.2 showed the opposite selectivity. Together, these tools enable cell-restricted, subunit-resolved interrogation of neurosteroid action on inhibitory microcircuits and provide a strategy to dissect how distinct GABAA receptor subclasses contribute to circuit function and therapeutic outcomes.

neuroscience↗

bioRxiv2026

CDS-BART: A BART-Based Foundation Model for mRNA Sequence Analysis

Summary: Recent advancements in artificial intelligence (AI) have led to the development of foundation models that interpret mRNA as a language. Notable examples include CodonBERT, hydraRNA, EVO2, and Helix-mRNA. These models demonstrate significant potential as powerful tools for mRNA research. However, to best of our knowledge, there is currently no publicly available AI model that is both easy to use and capable of analyzing mRNA sequences up to about 4kb, a length scale typical of many therapeutic mRNAs, including those encapsulated within lipid nanoparticls (LNPs). Thus, we propose CDS-BART, a user-friendly, open-source tool that integrates SentencePiece sub-word tokenization with the denoising sequence-to-sequence training of Bidirectional and Auto-Regressive Transformers (BART). CDS-BART was pre-trained on mRNA data from nine taxonomic groups provided by the NCBI RefSeq database. This comprehensive pre-training, coupled with BARTs denoising capability, ensures effective learning of codon usage, mRNA structure, evolution, and regulation. Thus, CDS-BART can ultimately deliver robust performance across a wide range of mRNA prediction tasks. Availability and ImplementationCDS-BART is released under the MIT License. Latest code is available via Github at https://github.com/mogam-ai/CDS-BART.

bioinformatics↗

bioRxiv2026

Identification of 4,5,6,7-Tetrabromo-1H-benzotriazole (TBB) as a Small Molecule MESH1 Inhibitor that Suppresses Ferroptosis

Ferroptosis is a regulated form of cell death driven by iron-dependent lipid peroxidation and contributes to diverse pathologies including ischemia-reperfusion injury and neurodegenerative disorders. Current ferroptosis inhibitors largely function as nonspecific radical-trapping antioxidants, limiting their clinical utility. We previously identified MESH1 as a key regulator of ferroptosis through its NADPH phosphatase activity. Here, we identify 4,5,6,7-tetrabromo-1H-benzotriazole (TBB) as a small molecule inhibitor of MESH1 with an IC50 value of 4.7 {+/-} 0.3 {micro}M. X-ray crystallography revealed the molecular determinants of TBB recognition which are corroborated through structure-activity relationships of TBB analogs. TBB protected multiple cell lines against ferroptosis in vitro, and this effect was mitigated by MESH1 knockdown, consistent with on-target activity. Furthermore, TBB reduced neuronal death in an ex vivo brain slice model of Alzheimers disease. Collectively, these findings establish TBB as a bona fide small-molecule MESH1 inhibitor that suppresses ferroptosis and establishes MESH1 as a promising therapeutic target. Graphical AbstractDepicting mechanism of TBB suppressing ferroptosis through the inhibition of MESH1. Figure Created with Biorender.com O_FIG O_LINKSMALLFIG WIDTH=131 HEIGHT=200 SRC="FIGDIR/small/706832v1_ufig1.gif" ALT="Figure 1"> View larger version (35K): org.highwire.dtl.DTLVardef@1fd60e9org.highwire.dtl.DTLVardef@1e56518org.highwire.dtl.DTLVardef@15010c2org.highwire.dtl.DTLVardef@17c313a_HPS_FORMAT_FIGEXP M_FIG C_FIG

biochemistry↗

bioRxiv2026

Microfluidic Agarose Microdroplets for DNA-Encoded Chemical Library Screening

DNA-encoded library (DEL) technology enables high-throughput small-molecule discovery but is typically performed using purified proteins under in vitro conditions that do not reflect native intracellular environments. Here, we present a microfluidic agarose -droplet platform for cellular-context DEL screening. The porous hydrogel droplets provide mechanically stable yet permeable microenvironments that protect weak protein-ligand interactions while enabling efficient buffer exchange and ligand diffusion. Importantly, mild cell permeabilization within droplets selectively retained chromatin-associated proteins, allowing screening directly in a cellular context. Using BRD4 as a model target, we validated intracellular ligand engagement by fluorescence imaging and super-resolution microscopy. Small-scale DEL screening selectively enriched JQ1 in both bead-based and cell-based formats, and large-scale DEL screening across millions of encoded compounds successfully identified hit molecules by sequencing. This agarose -droplet-based strategy expands DEL technology toward biologically relevant and chromatin-associated targets under near-native conditions.

bioengineering↗

bioRxiv2026

A macrophage-derived noncanonical WNT niche drives immune exclusion in pancreatic cancer

Background and AimsPancreatic ductal adenocarcinoma (PDAC) is characterized by profound immune exclusion and resistance to immunotherapy. Although WNT signaling has been implicated in PDAC, its cellular source within the tumor microenvironment and its contribution to immune suppression remain poorly defined. This study investigated whether myeloid-derived WNT signaling promotes PDAC progression. MethodsTranscriptomic data from human PDAC cohorts, including The Cancer Genome Atlas (TCGA), and published single-cell RNA sequencing datasets were analyzed. Macrophage-associated WNT5A expression in human PDAC biopsies was assessed using in situ hybridization and immunofluorescence. Macrophage-derived WNT secretion was genetically disrupted using macrophage-specific Porcn knockout mice in orthotopic and subcutaneous KPC tumor models. Lineage-resolved spatial organization of macrophage subsets was characterized using Ms4a3 fate-mapping double-reporter mice with immunofluorescence and imaging mass cytometry. Macrophages-CD8 T cells interactions were assessed using tumor-educated macrophage conditioned media, pharmacologic ARG1 inhibition, and in vivo CD8 T cell depletion. ResultsPDAC tumors with high macrophage signatures showed enrichment of noncanonical WNT signaling, and macrophage-associated WNT5A was detected in human biopsies. Disruption of macrophage-derived WNT secretion suppressed tumor growth, reversed immune exclusion, and enhanced cytotoxic CD8 T cell infiltration. Spatial lineage-resolved analysis demonstrated progressive accumulation of Hexb tissue-resident macrophages that dominated advanced lesions and formed a WNT-rich niche closely associated with Trem2Arg1 monocyte-derived macrophages. Mechanistically, macrophage-derived noncanonical WNT activated a JNK/c-Jun-ARG1 axis that inhibited CD8 T cell proliferation, an effect abolished by myeloid WNT loss. ConclusionsMyeloid-derived noncanonical WNT establishes a lineage-structured macrophage niche that enforces immune exclusion in PDAC. Targeting macrophage-restricted WNT signaling represents a promising strategy to reprogram the PDAC immune microenvironment.

cancer biology↗

bioRxiv2026

A pseudoenzyme controls the architecture of the extreme distal tip of motile cilia

Motile cilia are evolutionarily conserved organelles performing essential roles in development and tissue homeostasis. Unlike the core scaffold of motile cilia, the distal regions remain relatively less explored and display great diversity across species. Here, we describe a previously uncharacterized ciliary protein Jhc1, localizing at the extreme distal tip of multiciliated cell (MCC) cilia and encoded only in the genomes of non-mammalian vertebrates. Jhc1 is essential for cilia structure and length in Xenopus, an activity that is conserved in Jhc1 from reptiles and fish. Phylogenetic analysis and structure modeling suggests that Jhc1 arose by duplication and neofunctionalization of thiamine triphosphatase, and we show that residues crucial for that enzymes function have been lost and replaced by new residues essential for ciliary localization. These data provide new insights into the molecular mechanisms underlying the broad diversification of the structures at the tip of motile cilia during evolution.

cell biology↗

bioRxiv2026

Structural and Evolutionary Divergence of the RAG1/1L N-Terminal Zinc-Finger Domain

RAG1/2 catalyzes V(D)J recombination to assemble antigen receptor genes, yet the zinc-finger element at the RAG1 N terminus has remained structurally and functionally uncharacterized. Using NMR spectroscopy, we determined the structure of the RAG1 N-terminal zinc-finger domain (NZD; residues 89-223). NZD adopts a compact, zinc-dependent fold comprising four -helices organized into two interdigitated zinc-finger modules, ZFa and ZFb. Structural similarity searches across protein-structure databases revealed no solved homologs, establishing NZD as a previously undescribed zinc-finger fold. Comparative analyses show that NZD is broadly conserved across RAG1 and RAG1-like (RAG1L) proteins but has undergone lineage-specific remodeling, including the jawed vertebrate-specific acquisition of an additional -helix (H2). Guided by structure prediction, we identified two NZD-like types in Chapaev transposases; one is highly similar to the RAG1L NZD, supporting an evolutionary link between RAG1/RAG1L and Chapaev NZDs. Similarity between ZFa and the single-zinc ZAD further suggests that NZD originated from an ancestral single-zinc fold. Together, these findings provide a structural framework for mechanistic and evolutionary analyses of RAG1.

biochemistry↗

bioRxiv2026

Regulation of CtISWI activity by AutoN and HSS domain

Chromatin remodeler imitation switch (ISWI) plays an important role in regulating chromatin structure through sliding and spacing nucleosomes. Despite the enormous progress in regulatory elements and mechanisms of the activity of ISWI in recent years, there are still some unclear structures and mechanisms in different species. Here, we studied the ATPase activity and nucleosome binding affinity of Chaetomium thermophilum ISWI (hereafter referred to as CtISWIWT) and several mutants, further proving the importance of these mutated residues in the inhibition of AutoN. We also analyzed the effects of dsDNA and ssDNA on ATPase activity of CtISWI, suggesting the potential interaction between HSS and ATPase domain. Notably, we provided a predicted structural model based on the sequence of CtISWIWT, proposing a two-step activating mechanism of conformation change and activity regulation. Taken together, our findings elucidate a different model of ISWI self-maintenance and action, providing a new mechanism of regulation supporting chromatin remodeling. HighlightsO_LIStructural modeling of ISWI: a chromatin remodeler that couples to ATP hydrolysis to slide and space composition of nucleosome. C_LIO_LIThe ATPase activity of ISWI can be stimulated by exogenous DNA, with opposite promoting effects by dsDNA and ssDNA. C_LIO_LIThe mechanism by which ISWI is activated upon binding with nucleosome has been the subject of debate, and a more comprehensive mechanism for regulation of ISWI activity. C_LI SignificanceIn the past decades, a variety of regulatory mechanisms of the activity of chromatin remodeling factor ISWI have been proposed. Based on the hypothesis of nucleosome complex structure analysis, these studies attempted to explore the mechanism of chromatin remodeling, a gene expression regulation activity. However, previous studies have basically focused on the binding and regulation mechanism of ISWI ATPase domain and nucleosomes, without mentioning the activity mode of full-length ISWI. Therefore, our study mainly focuses on the nearly full-length ISWI containing HSS domain, exploring the mechanism of the active state transition of ISWI in remodeling activities from this perspective. It enriches and supplements the research on chromatin remodeling, an important physiological activity.

biochemistry↗