Biology subjects

Zheng, T.

Publications and source records attributed to Zheng, T..

At least 19 recordsLinked to original sources

bioRxiv2026

Digital molecular kinetics enabled by large-scale nanopore arrays for multidimensional biophysical profiling

While widely used, traditional technologies like surface plasmon resonance (SPR) are limited by narrow temporal windows (transient capture and baseline drift), dynamic heterogeneity, and poor physiological temperature performance. Meanwhile, early nanopore approaches are often constrained by limited throughput and heavy reliance on customized modification schemes. Here, we present a digital molecular kinetics (DMK) platform based on large-scale nanopore arrays. By introducing a universal coupling and probe reporting system, DMK achieves broad versatility across diverse molecular pairs, including proteins, peptides, small molecules, DNA, and polymerase complexes. In addition to accurately recovering classical SPR association and dissociation rate constants, by harnessing massive single-molecule event analysis, DMK breaks traditional performance boundaries: it facilitates robust thermodynamic-kinetic profiling across a wide temperature range, resolves distinct conformations in heterogeneous samples, enables ultra-low dissociation rate quantification via maximum likelihood estimation, and reveals energy wells via voltage gradients for binding analysis against environmental perturbations. Furthermore, DMK enables the capture of rapid binding events missed by SPR, offering a new perspective on molecular interaction complexity. This platform offers an effective alternative and upgrade to SPR, opening a digital paradigm for complex molecular analysis and drug discovery.

biophysics↗

bioRxiv2026

NeoOmni Atlas: an integrated database for pan-cancer neoantigen derived from proteogenomics analysis

Tumor neoantigens derived from diverse molecular aberrations are important targets for personalized cancer immunotherapy, but existing resources incompletely integrate mass-spectrometry-supported canonical and non-canonical antigen evidence across cancer types. NeoOmni Atlas is an interactive pan-cancer T-cell epitope resource, built via proteogenomic reanalysis of 7,561 immunopeptidomics datasets comprising 511 million raw spectra from 2,341 samples across 26 cancer types. The analysis yielded 872,414 eluted canonical peptides and 198,961 non-canonical peptides spanning 18 molecular alteration classes, along with 759,386 unique ligands presented by 322 human leukocyte antigen (HLA) alleles. Relative to existing repositories, NeoOmni Atlas covers a broader range of cancer types, includes 60 additional HLA alleles, and catalogs 369,781 novel ligands. A computational tumor-specific filtering framework identified 316,126 tumor-associated epitopes and 61,231 tumor-specific epitopes. Tumor-specific epitopes showed stronger predicted binding affinity than tumor-associated epitopes for HLA class I A and B alleles, and 65 conserved tumor-specific epitopes recurrent across more than 10 tumor types represent potential shared antigen candidates. NeoOmni Atlas also prioritizes candidate tumor-associated antigens including PMEL (gp100:209-217) and CSPG4, and supports browsing, searching, and downloading by cancer type, human leukocyte antigen allele, peptide sequence, and source event. NeoOmni Atlas is freely accessible at http://modinfor.com/NeoOmni-Atlas/.

bioinformatics↗

bioRxiv2026

Foveation as self-supervision signal: Blur masks beat blank masks for learning robust visual representations

The primate retina is strikingly non-uniform, with receptor density falling off sharply from fovea to periphery. Every eye-movement brings a previously low-acuity peripheral area to high-acuity foveal processing. We hypothesize that this process provides a natural self-supervision signal, enabling representation learning by predicting fine details in the periphery. We implement this in a SimMIM-style vision transformer, replacing its blank masks (ViT-Blank) with a uniform blur mask (ViT-Blur) and further with retinal masks in which a foveal patch is randomly selected, and all other patches are progressively blurred based on eccentricity from the foveal patch (ViT-Retina). ViTs were pre-trained to reconstruct the full-resolution image from the corrupted input and then fine-tuned on clean images for classification. ViT-Blur and ViT-Retina outperform ViT-Blank on the pre-training reconstruction task while controlling for retained information from the input across corruption types. Critically, they also outperform ViT-Blank on downstream classification, showing that they learn representations that generalize better. The ViT-Blur and ViT-Retina are also more robust in impoverishment conditions such as higher mask ratios, fewer pre-training epochs, smaller training sets, and test time image corruptions. Using additive band-limited noise, we discovered that ViT-Blank relies on higher spatial frequencies compared to ViT-Blur and ViT-Retina, and we show this to be the likely cause of poorer generalization: the centroid of a model's spatial frequency tuning is negatively correlated with its classification accuracy ($r = -0.73$). We further show that a closed-form linear-ridge encoder derived from the same reconstruction objective reproduces this tuning ($r = 0.88$). Overall, our experiments show the promise of a biologically-inspired self-supervision objective for learning robust visual representations.

neuroscience↗

bioRxiv2026

Systemic tumor-cell reprogramming converts solid tumors into in situ biofactories for immunotherapy

A central challenge in oncology is delivering potent drugs to tumors without harming healthy tissues. We therefore asked whether tumor cells themselves could be genetically programmed to produce therapeutic molecules directly within the tumor. We present LENTRA (LENtiviral Tumor-Reprogramming Activator), an antigen-targeted lentiviral platform that enables selective transduction and genetic modification of tumor cells in vivo. Following intravenous administration, LENTRA achieves tumor restricted expression of immune checkpoint inhibitors, cytokines, or therapeutic enzymes in multiple murine solid tumor models. Local production of anti CTLA 4 or IL 12 triggered potent antitumor responses while avoiding systemic toxicities. Tumor restricted secretion of sialidase enhanced dendritic cell and T cell infiltration, and reprogrammed tumor associated macrophages toward an immunostimulatory phenotype, resulting in tumor regression and durable immune memory, including in tumors with heterogeneous antigen expression. In patient derived tumor explants, LENTRA mediated efficient transduction, immune remodeling, and reduced tumor viability. By engineering tumors to produce therapeutic proteins, LENTRA converts resistant tumors into autonomous therapeutic sources and active immune hubs, achieving local TME reprogramming and systemic antitumor immunity with an improved safety profile.

cancer biology↗

bioRxiv2026

An RBP-J-heparan sulfate-dependent gatekeeper directs macrophage fate between inflammatory regulation and osteoclastogenesis

Macrophages in bone possess a unique bi-potential capacity. Different from their primary roles in inflammation and immunity, these cells can differentiate into bone-resorbing osteoclasts. However, it remains unclear how macrophages determine which function to engage in bone, especially when exposed to the same stimulus, such as TNF, which can drive both pathways. Understanding these mechanisms is particularly important in inflammatory bone diseases, such as rheumatoid arthritis, where inflammation and bone resorption are hallmarks. Here, we identified an RBP-J-Hs2st1-2-O-sulfated heparan sulfate (HS)-IFN{beta} ; dependent molecular network that acts as a gatekeeper balancing macrophage fate inclinations in response to TNF. This network integrates cellular outside-in, inside-out, and relayed outside-in pathways. RBP-J deficiency in macrophages shifts TNF action from inflammatory regulation to osteoclastogenesis. Hs2st1, the exclusive biosynthetic enzyme for 2-O sulfation of HS, is a key target suppressed by RBP-J. Loss of Hs2st1 significantly reduces inflammatory osteoclastogenesis and arthritic bone erosion without affecting physiological bone mass. Elevated Hs2st1 expression and 2-O sulfation shift macrophages toward an osteoclastogenic fate, and vice versa. We further identified residues in IFN{beta} ; that are responsible for binding HS. Mutation of these sites diminished HS binding, augmented type I IFN response, and more strongly suppressed osteoclastogenesis. Our findings reveal a previously unrecognized molecular program fine-tuning macrophage fate and function, and highlight potential therapeutic strategies for inflammatory diseases with bone defects.

immunology↗

bioRxiv2026

A patient-centric therapeutic paradigm uncouples prostate cancer suppression from systemic metabolic collapse

The clinical benefits of cancer therapies are often compromised by the tolerable adverse effects that impair systemic organismal health and may evolve into latent life threats. Here, we identified profound abiraterone-induced but androgen-independent metabolic perturbations in prostate cancer patients and developed Lifehug-9892 to balance tumor therapy with systemic metabolic homeostasis. By integrating population cohorts with high-resolution metabolomics, we demonstrate that abiraterone induces profound systemic lipidomic dysregulation, characterized by the massive, pathological accumulation of desmosterol. Abiraterone inhibits but stabilizes DHCR24, leading to a metabolic trap in patients showing elevated levels of both desmosterol and cholesterol. Desmosterol accumulation is highly lipotoxic, potently triggering endothelial cell senescence and necrosis, macrophage foam cell formation, murine atherosclerosis, and hepatic senescence. To mechanistically uncouple and therapeutically rescue this systemic metabolic collapse, Lifehug-9892 was rationally designed to selectively retain on-target CYP17A1 inhibition while completely sparing DHCR24 function. Lifehug-9892 maintains potent tumor-suppressive activity while fully preserving the desmosterol-cholesterol metabolic axis and preventing systemic cardiovascular and hepatic damage. Our study uncovers a critical mechanistic link between drug-induced metabolic dysregulation and organismal health in cancer patients, providing a biochemical framework for developing patient-centric targeted therapies that preserve host homeostasis.

cancer biology↗

bioRxiv2026

BCIJelly: An integrated ecosystem for brain-computer interface research

Brain-computer interface (BCI) research relies on multistage computational pipelines, but progress has been slowed by fragmented data formats, heterogeneous decoder implementations and hardware-specific deployment toolchains. Here, we introduce BCIJelly, a unified ecosystem that standardizes 18 BCI datasets into AI-ready inputs and integrates 15 benchmark decoders, 80 reusable modules, automated architecture search (AAS) and hardware-aware neuromorphic deployment. Our AAS constructs task-specific decoders without manual design and extends into a large language model (LLM)-driven closed-loop mode supporting single-task, multitask and cross-species decoder design. A single-command pipeline compiles trained decoders for neuromorphic hardware, reducing power consumption by 30 to 50 times while preserving decoding performance. An interactive visualization software enables code-free exploration of neural recordings and decoding outputs. BCIJelly is validated across five BCI paradigms (motor, visual, speech, emotion and auditory) in humans, macaques and mice, providing an extensible ecosystem connecting data standardization, decoder development, systematic evaluation and hardware-aware deployment for BCI research.

neuroscience↗

bioRxiv2026

A Compact, Standalone & Battery-Powered 3D Organoid-on-Chip System with Programmable Flow Control

Organoids-on-chip combine the 3D complex microenvironment and cellular composition of organoids with microfluidic flow, increasing nutrient-waste exchange and mimicking the contributions of in vivo interstitial and vascular flow. However, the widespread adoption of organoid-on-chip platforms is limited by the lack of incubator-friendly flow control systems. Existing approaches often rely on commercially available syringe or peristaltic pumps, but these are bulky, lack scalability, and present a significant barrier for clinical translation. To circumvent these issues, we present the Compact Active Perfusion Standalone Organoid-on-Chip (CAPS-OC) platform, a fully integrated and battery-powered microfluidic system capable of culturing organoids in active media flow. To achieve this, we introduce a novel low-power mechanism of pressure pulse generation using an off-the-shelf compact rotary actuator (CRA), and package it into a compact electromechanical assembly. This assembly provides timed pneumatic inputs to achieve programmable control of membrane-based peristaltic pumps, with [~]100 {micro}L/hr dynamic range achieved on a custom microfluidic organoid chip. We biologically validated this system by culturing pancreatic cancer organoids derived from a KrasLSL-G12D/+; Trp53LSL-R172H/WT; Pdx1-Cre (KPC) genetically engineered mouse model. We found that our chip enhances proliferation and helps sustain a population of larger (>150 {micro}m) organoids compared to standard dome based static culture. Additionally, through immunostaining, we observe that KPC organoids cultured in the chip show more aggressive PDAC phenotype with reduced nuclear expression of GATA6, whereas organoids in static culture retain less aggressive classical- like subtype. Finally, testing of a RAS inhibitor drug, daraxonrasib, on the KPC organoids on chip showed size-based sensitivity elucidating the impact of active perfusion on the drug diffusion kinetics. Altogether, we establish CAPS-OC as a valuable tool for the bioengineering community and for clinically translating organoid model systems.

bioengineering↗

bioRxiv2026

Spatial Patterning of Otic Vesicles in Human Inner Ear Organoids

During development axial patterning of the otic vesicle sets up the blueprint for the adult inner ear. While human inner ear organoids recapitulate the initial steps of ear formation, whether and how vesicles are properly regionalised remains unknown. Here, we combine re-analysis of published single-cell transcriptomic datasets with 2D and 3D imaging to assess axial patterning in human stem-cell-derived otic vesicles using a new PAX2-reporter line. We find that the transcriptional signatures of individual cells do not conform to clearly defined regional characteristics, with some cells co-expressing conflicting regional markers, while markers that should be co-expressed are not. Some vesicles establish spatially segregated molecular domains. However, patterning is incomplete, stochastic, and restricted to a subset of vesicles. Within the same aggregates, patterned axes lack consistent orientation. Together, our findings point to incomplete segregation of transcriptional programs that are mutually exclusive in vivo and to the absence of morphogen gradients that are crucial for otic vesicle patterning. >One sentence summaryIn human inner ear organoids, otic vesicles show incomplete and disorganized regionalisation pointing to fundamental limits of self-organization, while suggesting new routes to increase cell complexity in vitro.

developmental biology↗

bioRxiv2026

Decoding the oxytocinergic and behavioral signatures of milk ejection

Oxytocin-mediated milk ejection (ME) is pivotal to effective breastfeeding and productive health, yet behaviorally decoding and revealing neural mechanisms of ME remains challenging. Here, we combined in vivo calcium imaging and intramammary pressure recording to uncover the temporal connections between episodic activity of oxytocin neurons and ME in conscious lactating rats. Leveraging the association and behavioral responses in dam and pup, we developed a supervised machine learning framework (ME Decoder) to enable automated analyses of ME. Inspired by its interpretable features, we defined the activity-coupled dam-pup interactions (ADPI), manifested by high kyphosis of the dam followed by pup treading and stretch, as the behavioral signatures of ME. By ME Decoder and ADPI analyses, we detected reduced ME but unaffected activity of oxytocinergic neurons after systemic blockade of oxytocin receptor. Our study uncovers the oxytocinergic and behavioral signatures of ME and provides a generalizable approach for further investigation.

neuroscience↗

bioRxiv2026

The genetic architecture of dementia risk: how Alzheimer's disease vulnerability converges on lipid metabolism and immune cell networks

Although genome-wide association studies (GWAS) have identified numerous dementia risk loci, their cell-type and tissue-specific contexts remain largely unresolved. We introduced HPA GeneSet Explorer, a statistical pipeline designed to systemically map Genome wide association study (GWAS) disease risk genes across the Human Protein Atlas (HPA). This approach generates a multiscale transcriptomic map of genetic risk, spanning systemic organs, brain regions, and cell types. Applying this framework to Alzheimers disease (AD), Lewy body dementia (DLB), and Frontotemporal dementia (FTD) revealed convergent neuronal enrichment in all three diseases. In addition, we identified AD-specific enrichment in immune system and liver associated gene modules, along with DLB-specific enrichment in ciliary modules. By mapping these vulnerabilities in non-demented samples, we provide a blueprint of the baseline vulnerability hotspots that can precede clinical neurodegeneration, offering new targets for disease-specific therapies and biomarker discovery.

neuroscience↗

bioRxiv2026

A Comprehensive Computational Model of the Human head for Designing and Optimizing Visual Brain-Machine Interfaces

Brain-machine interfaces (BMIs) for vision restoration require models that accurately simulate the anatomy and electrical properties of visual pathways. However, current models focus only on isolated structures, such as the retina or brain, and overlook surrounding tissues. Here, we present a comprehensive computational model of the human head, incorporating the entire visual pathway--including the eye, optic nerve, and brain--along with critical neighboring tissues such as the orbit, paranasal sinuses, enabling precise simulations. Validation using human and large animal data demonstrated a strong correlation between the simulated and measured electrical potentials. Component elimination analysis revealed that the optimized comprehensive model outperformed simplified versions. The models utility was demonstrated through multiple applications: (1) comparative analysis of electrical neuromodulation technologies for optic neuropathy, revealing the filed intensity limitations of noninvasive approaches and the safety concerns of invasive intraorbital approach; (2) identification of optimal stimulation site, revealing that transnasal stimulation at the optic chiasm outperformed traditional approaches; and (3) in silico design of electrode arrays for optic nerve prosthetics, demonstrating theoretical advantages in invasiveness and visual field coverage compared to existing retinal and cortical prosthetics. This validated and versatile computational resource supports the development of neuromodulation strategies and visual BMI technologies.

bioengineering↗

bioRxiv2026

Coordinated phase separation and phase transition underlie synaptic ribbon condensate formation and plasticity

Mesoscale molecular apparatuses with diverse functions are widespread in cells. How mesoscale cellular apparatuses are formed and regulated is poorly understood. The synaptic ribbon in sensory neurons, which can dynamically adjust its size and shape in response to light or sound, is a mesoscale molecular assembly. In this study, we demonstrate that RIBEYE, the backbone protein of synaptic ribbons, via combined ordered and disordered interactions, forms micron-sized dynamic molecular assemblies. Integrated cryo-electron microscopy and tomography studies revealed that the N-terminal SAM domain and the C-terminal B domain of RIBEYE form distinct nanoscale filaments and further assemble into ribbon-like architectures via phase transition. Unexpectedly, the N-terminal intrinsically disordered region of RIBEYE softens the solid mesoscale ribbon structures via phase separation. The mesoscale size and shape of the RIBEYE condensate are bidirectionally tuned by physiological modulators such as Piccolino and CtBP1, linking synaptic ribbon structural plasticity to functional adaptability. Thus, our study demonstrates that combined phase transition and phase separation of nanoscale protein oligomers can build mesoscale functional cellular apparatuses.

biochemistry↗

bioRxiv2026

Extensive genomic diversity in Desulfovibrio species reveals species-specific functional traits associated with disease

Desulfovibrio spp. are associated with inflammatory diseases and human health, yet limited representative genomes and isolates hinder our understanding of their role in disease. Here, we assembled a comprehensive database of 2,658 Desulfovibrio genomes across 90 diseases and 32 countries, including 24 human isolates. Genomic analyses showed extensive species diversity and revealed disease-associated functional traits, including flagellin and virulence genes (i.e. ureases). Flagellin-mediated Toll-like receptor 5 activation was species-specific and D. desulfuricans flagellin downregulated TGF-beta signalling in murine small intestinal organoids, suggesting impaired immune tolerance. Additionally, we investigated genomic capacity for hydrogen sulfide (H2S) production, a main Desulfovibrio metabolite. While health- and disease-associated Desulfovibrio spp. mainly encoded dissimilatory sulfate reduction, tetrathionate metabolism-encoding bacteria were exclusively detected in inflammatory bowel diseases, including Proteus mirabilis and Morganella morganii. Overall, our study provides a comprehensive genomic Desulfovibrio resource and identifies new links associating strain variation, functional traits and H2S-production with inflammatory diseases.

genomics↗

bioRxiv2026

Breaking β-sheets in FUS prion-like domain preserves phase separation and function but prevents aggregation and toxicity

The RNA-binding protein Fused in Sarcoma (FUS) undergoes phase separation associated with RNA processing. However, the prion-like low complexity (LC) domain of FUS forms solid-like aggregates in neurodegenerative diseases. Whether the formation of {beta}-sheet structure associated with pathology is also physiologically/functionally relevant is debated. Similarly, if mislocalization alone or concomitant aggregation is responsible for FUS gain-of-function toxicity remains to be probed. Here, we introduce {beta}-sheet breaking proline residues into FUS LC with the goal of preventing cross-{beta}-driven aggregation without disrupting essential functions and phase separation. {beta}-sheet-deficient FUS variants maintain native-like global motions, disorder, and phase separation, but no longer show a liquid-to-solid transition (LST). Biochemical partitioning, cellular localization, and auto- and cross-regulatory functions of FUS all remain essentially unchanged. Conversely, FUS-induced neurodegeneration in several Drosophila models is drastically reduced. These findings suggest a strategy for mitigating disease-related toxicity through backbone structure modulation to prevent prion-like domain protein aggregation. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=198 SRC="FIGDIR/small/706410v1_ufig1.gif" ALT="Figure 1"> View larger version (53K): org.highwire.dtl.DTLVardef@d15f63org.highwire.dtl.DTLVardef@1cd6221org.highwire.dtl.DTLVardef@e58126org.highwire.dtl.DTLVardef@181ec67_HPS_FORMAT_FIGEXP M_FIG C_FIG SUMMARYThe RNA-binding protein Fused in Sarcoma (FUS) undergoes phase separation as part of its physiological function but can aberrantly aggregate into solid-like assemblies in amyotrophic lateral sclerosis and frontotemporal dementia. To dissect the role of {beta}-sheets in both function and pathological transition, we engineered {beta}-sheet-preventing FUS variants via targeted proline residue insertions in the prion-like disordered region. These variants retained native structure, motions, and phase behavior yet showed dramatically reduced aggregation, both as an isolated prion-like domain and in full-length FUS. Crucially, these variants maintained a panel of FUS cellular functions that depend on FUS condensation but prevented FUS toxicity in fly models of neurodegeneration. Our findings implicate {beta}-sheets as key drivers of FUS condensate maturation and neuronal toxicity, highlighting {beta}-sheet modulation as a therapeutic strategy against FUS-related neurodegeneration. HIGHLIGHTSO_LITargeted proline additions disrupt {beta}-sheet formation in FUS without altering native conformations, dynamics, or phase separation behavior C_LIO_LI{beta}-sheet-deficient FUS variants prevent aggregation and liquid-to-solid transitions while retaining key biological functions C_LIO_LIIn vivo models reveal attenuated toxicity of {beta}-sheet-deficient FUS in Drosophila C_LIO_LI{beta}-sheets are identified as central drivers of condensate maturation and neuronal death, offering a therapeutic entry point for modulating prion-like domain pathology C_LI

biochemistry↗

bioRxiv2026

Rab32/Rab38-positive Lysosome-Related Organelle degrades lipid droplet in hepatocytes by microautophagy

Rab32 and Rab38 are paralogous small GTPases involved in the biogenesis of lysosome-related organelles (LROs), yet their roles in hepatic lipid metabolism remain poorly defined. Here, Rab32 and Rab38 double-knockout (DKO) male mice exhibited an age-dependent increase in body weight accompanied by hepatic lipid accumulation, suggesting impaired hepatic lipid processing. In AML12 hepatocytes, Rab32 and Rab38 localized to ring-like, LAMP1-positive structures characteristic of LROs, whose size increased with cell confluence. Pharmacological inhibition of lysosomal acid lipase with orlistat led to the accumulation of lipid droplets (LDs) within Rab32/38-positive LROs, indicating that LD degradation occurs in these compartments. Additional treatment with bafilomycin A1 revealed invagination-like internal membrane structures within enlarged LROs. These processes were not affected by artificial inhibition of macroautophagy, highlighting the involvement of microautophagy. Ring-like signals positive for phosphatidylinositol 3-phosphate (PI3P) or phosphatidylinositol 3,5-bisphosphate (PI(3,5)P2) were detected within or adjacent to LRO membranes, and LDs were frequently associated with these structures, suggesting a role for PI3P and PI(3,5)P2 in internal membrane formation. Vps4B was also required for efficient LD incorporation. Consistently, Rab32/38 double-knockdown (DKD) AML12 cells exhibited increased lipid accumulation, indicating impaired LD engulfment. Together, these findings identify Rab32/38-positive LROs as a structural platform for microautophagy-mediated lipid droplet degradation in hepatocytes.

cell biology↗

bioRxiv2026

Prime-InDel version 1: A web tool providing InDel markers for targeted regions narrowing

While high-density SNP genotyping enables genome-wide assays in rice (Oryza sativa L.) and other crops, PCR-based markers--particularly those derived from insertion-deletion (InDel) variations--remain crucial for fine-mapping. Currently, readily available primer information for high-density InDel rice markers is still limited. We present the first version of PrimeInDel (https://rfgb.rmbreeding.cn/search/variation/primeIndel), an online tool integrating three sets of InDel markers: an 8K-set and a 316K-set from the 3K Rice Genomes (3K-RG) project, and a 22K-set compiled from published literatures. In user cases, primers from PrimeInDel proved highly effective, narrowing a cold-tolerance QTL (qSR2) from 2.7 Mb to 200 kb and a heading-date QTL (qDeh1.1) from 239.5 kb to 83.6 kb. Our work provides the community with a robust, PCR-based InDel primer, accessible via an online data set, which will facilitate germplasm genotyping and gene identification in rice breeding.

plant biology↗

bioRxiv2026

The glycine-arginine-rich motif of 53BP1 modulates RNA interactions necessary for its liquid-liquid phase separation during DNA Damage Response

The DNA damage response relies on the rapid assembly of repair factors into foci with properties of liquid-liquid phase separation, driven by de novo transcription of damage-induced RNAs. 53BP1 is a key component of these condensates, yet the molecular determinants driving this process remain unknown. Here, through computational, structural and in vitro approaches, we identify the oligomerization domain of 53BP1 and its glycine-arginine-rich (GAR) motif as crucial for RNA interactions and phase separation. Biophysical characterization reveals that 53BP1-RNA condensates can progressively mature into a more stable state, and that GAR mutants display aberrant material properties. Using a cellular model of telomere fusion events, we demonstrate that the GAR motif is essential for 53BP1-mediated DNA repair, which depends on the combined contributions of RNA binding and appropriate condensate biophysical properties. Therefore, RNA-driven 53BP1 condensation is functionally required to maintain genome integrity.

biophysics↗