Biology subjects

Cai, Y.

Publications and source records attributed to Cai, Y..

At least 73 records · Page 4Linked to original sources

bioRxiv2025

Transient Poly(ADP-Ribose) Triggers FUS Condensation Hysteresis via a Prion-Like Mechanism

Hysteresis--where a system retains memory of a transient stimulus--is common in signaling but can also arise in intracellular organization. DNA repair foci, a type of biomolecular condensate, are initiated by the short-lived noncanonical nucleic acid poly(ADP-ribose) (PAR). PAR recruits proteins with prion-like domains (PrLDs), such as Fused in Sarcoma (FUS), and initiates their condensation, which persists even after PAR degradation. How FUS transitions from PAR-dependent to PAR-independent condensation remains unclear. Here, we show that PAR binding triggers a conformational switch in FUS, enabling sustained condensation. PAR binds to the C-terminal arginine-rich region of FUS, displacing intramolecular contacts, and exposing the N-terminal PrLD. This conformational opening allows PrLD interactions in trans, stabilizing condensates independently of PAR. FUS thus undergoes a regulated, nucleated conformational conversion--reminiscent of classical prions. This mechanism implies a paradigm of nucleic acid-induced conformational memory that may underlie hysteresis in intracellular organization in health and disease. HIGHLIGHTS[bullet] PAR-initiated FUS condensation follows a bi-modular mechanism involving both FUS termini. [bullet]Simulations predict and experiments confirm PAR disrupts FUS intramolecular contacts. [bullet]Upon condensation, FUS adopts a conformation with its N-terminus open for interactions. [bullet]N-terminal interactions maintain FUS condensation when PAR degrades during DNA repair.

molecular biology↗

bioRxiv2025

Genomic Touchstone: Benchmarking Genomic Language Models in the Context of the Central Dogma

The emergence of genomic language models (gLMs) has revolutionized the analysis of genomic sequences, enabling robust capture of biologically meaningful patterns from DNA sequences for an improved understanding of human genome-wide regulatory programs, variant pathogenicity and therapeutic discovery. Given that DNA serves as the foundational blueprint within the central dogma, the ultimate evaluation of a gLM is its ability to generalize across this entire biological cascade. However, existing evaluations lack this holistic and consistent framework, leaving researchers uncertain about which model best translates sequence understanding into downstream biological prediction. Here we present Genomic Touchstone, a comprehensive benchmark designed to evaluate gLMs across 36 diverse tasks and 88 datasets structured along the central dogmas modalities of DNA, RNA, and protein, encompassing 5.34 billion base pairs of genomic sequences. We evaluate 34 representative models encompassing transformers and convolutional neural networks, as well as emerging efficient architectures such as Hyena and Mamba. Our analysis yield four key insights. First, gLMs achieve comparable or superior performance on RNA and protein tasks compared to models pretrained on these molecules. Second, transformer-based models continue to lead in overall performance, yet efficient sequence models show promising task-specific capabilities and deserve further exploration. Third, the scaling behavior of gLMs remains incompletely understood. While longer input sequences and more diverse pretraining data consistently improve performance, increases in model size do not always translate into better results. Fourth, pretraining strategies, including the choice of training objectives and the composition of pretraining corpora, exert substantial influence on downstream generalization across different genomic contexts. Genomic Touchstone establishes a unified evaluation framework tailored to human genomics. By spanning multiple molecular modalities and biological tasks, it offers a valuable foundation for guiding future gLM design and understanding model generalizability in complex biological contexts.

bioinformatics↗

bioRxiv2025

Visual Working Memory Guides Attention Rhythmically

How does internal representation held in visual working memory (VWM), known as the attentional template, guide attention? A longstanding debate concerns whether only one (Single-Item-Template theory) or multiple (Multiple-Item-Template theory) items serve as attentional templates simultaneously. Here we propose a Rhythmic-Item-Template hypothesis, successfully reconciling these seemingly contradictory theories. Using the classical VWM-guided attention task, we found that two VWM items alternately dominate behavioral guidance in theta-rhythmic (4-8 Hz), with anti-correlated activation states in time, and more importantly, this rhythmic oscillation was not driven by the retro-cue processing. Neural recordings revealed that occipital alpha-oscillation (8-14 Hz) governed item-specific prioritization and its amplitude closely tracked subjects behavioral guidance, while frontal theta-oscillations phase-led and coupled with occipital alpha-oscillations during the item transition. Our Rhythmic-Item-Template results not only resolve previous Single-Item-Template versus Multiple-Item-Template debate but also advance our understanding of how distributed brain rhythms coordinate flexible resource allocation in multi-item memory systems.

neuroscience↗

bioRxiv2025

A bottom-up approach to understanding ultrasound mediated blood-brain barrier opening using long and short pulses

Ultrasound-mediated blood-brain barrier (BBB) opening is promising for non-invasive, localized, and reversible drug delivery to the brain. However, the underlying mechanisms remain unclear, particularly at microscopic level in real time. Recently developed short-pulse ultrasound enhances safety by reducing side effects compared to conventional long-pulse ultrasound. Using vessel-mimicking microchannels cultured with brain endothelial monolayers, we directly observed bubble dynamics and cellular bioeffects under flow conditions. Intriguingly, cyclic jetting during stable cavitation occurs at long-pulse mode, accompanied by a few localized cell detachments and extensive sonoporation. In contrast, short-pulse ultrasound induced milder, uniform bubble dynamics, reversible sonoporation and calcium signaling, promoting safer BBB modulation. In vivo two-photon imaging and histology in mice confirmed these findings, showing that long-pulse ultrasound enabled higher drug delivery efficiency but caused localized endothelial damage, while short-pulse ultrasound facilitated uniform delivery and faster BBB recovery. The differential bubble dynamics and cellular responses correlated well between in vitro and in vivo models. This study establishes a cross-scale framework for real-time analysis of ultrasound-mediated BBB opening, revealing key biophysical factors governing safety and efficacy. The findings provide guidance for the optimization of ultrasound protocols for vascular drug delivery, with potential applications in treating brain tumors, neurodegenerative diseases, and other disorders.

biophysics↗

bioRxiv2025

Ultra-high field strength electroporation enables efficient DNA transformation and genome editing in nontuberculous mycobacteria

Efficient DNA delivery is essential for genetic manipulation of mycobacteria and for dissecting their physiology, pathogenesis, and drug resistance. Although electroporation enables transformation efficiencies exceeding 105 CFU per {micro}g DNA in Mycobacterium smegmatis and Mycobacterium tuberculosis, it remains highly inefficient in many non-tuberculous mycobacteria (NTM), including Mycobacterium abscessus. Here, we discovered that NTM such as M. abscessus exhibit exceptional tolerance to ultra-high electric field strengths, and that hypertonic preconditioning partially protects cells from electroporation-induced damage. Using ultra-high electric field strength (3kV/mm) electroporation, we achieved dramatic improvements in plasmid transformation efficiency--up to 106-fold in M. abscessus, 83-fold in Mycobacterium marinum, and 24-fold in Mycobacterium kansasii--compared to standard conditions (1.25 kV/ mm). Transformation efficiency was further influenced by the choice of selectable marker. Ultra-high field strength electroporation also markedly enhanced allelic exchange in M. abscessus expressing Che9c RecET recombinases, increasing recovery of gene deletion mutants by over 1,000-fold relative to conventional electroporation. In parallel, oligonucleotide-mediated recombineering for targeted point mutations produced nearly 10,000-fold more mutants under ultra-high field conditions. Together, these findings establish ultra-high field electroporation as a robust, broadly applicable platform for genetic engineering of NTMs. This method substantially enhances transformation efficiency and enables construction of advanced genetic tools--including expression libraries and CRISPRi knockdown libraries--in species that have historically resisted genetic manipulation. ImportanceInfections caused by non-tuberculous mycobacteria (NTM), including Mycobacterium abscessus, are increasing globally, yet genetic manipulation of these pathogens remains technically challenging due to inefficient DNA delivery and low gene editing success. The ultra-high electric field strength electroporation strategy described here overcomes these barriers, enabling dramatic improvements in both transformation and genome editing efficiency. This advance paves the way for high-throughput functional genomics in NTMs, including the construction of genome-wide knockout, CRISPRi knockdown, and expression libraries. Broad adoption of this approach will accelerate discovery of genetic determinants of virulence and drug resistance, facilitating the development of antimicrobials and vaccines.

microbiology↗

bioRxiv2025

Single-stranded DNA binding proteins are essential components of the architectural LDB1 protein complex

Transcriptional enhancers are brought into proximity with promoters via chromatin looping. The architectural transcription cofactor LDB1 facilitates spatial connectivity among enhancers and promoters but whether this occurs through simple dimerization or requires partner molecules is unknown. Here we investigated single-stranded DNA binding proteins (SSBPs), known LDB1 interactors, in regulating LDB1-mediated chromatin looping and transcription. SSBP2, SSBP3, and SSBP4 colocalize with LDB1 genome wide. Among these, only SSBP3 is essential for erythroid cell viability, LDB1 function, and transcription. LDB1, but not single-stranded DNA, is the predominant genome-wide tether of SSBP3 to chromatin. Notably, SSBP3 depletion for under one hour in SSBP2/4 knockout cells globally weakened LDB1-dependent chromatin loops and lowered nascent transcription without impacting LDB1s chromatin binding. Chromatin tethering experiments revealed SSBP3 and LDB1 mutually depend on each other to form looped contacts. SSBP3 stabilizes LDB1 homodimers in solution providing a possible mechanism of action. In sum, SSBPs emerge as key functional components of the architectural LDB1 complex, shedding new light on the regulation of enhancer-promoter interactions and gene expression.

genomics↗

bioRxiv2025

β-Glucan Modulates Monocyte Plasticity and Differentiation Capacity to Mitigate DSS-Induced Colitis

Trained immunity involves the reprogramming of innate immune cells after an initial exposure, resulting in heightened inflammatory responses to subsequent stimuli and enhanced bactericidal capacity during infection. However, this proinflammatory state could also exacerbate chronic conditions like inflammatory bowel disease (IBD), which is characterized by persistent inflammation and microbial imbalance. It remains unclear how trained immunity influences IBD pathogenesis and whether it can be harnessed therapeutically. In our study, pretreatment with {beta}-glucan reprogrammed bone marrow hematopoietic progenitors and peripheral monocytes, inducing a profound shift in monocyte plasticity and significantly reducing the severity of dextran sulfate sodium (DSS)-induced colitis. Adoptive transfer of bone marrow or peripheral monocytes from {beta}-glucan-trained mice into naive mice conferred robust protection against colitis, demonstrating that this protective effect is transferable. Trained mice also displayed improved clearance of intestinal bacterial infections. Single-cell RNA sequencing revealed an expansion of reparative Cx3cr1 macrophages derived from Ly6Chi monocytes, correlating with accelerated colonic epithelial regeneration. Collectively, these findings reveal how {beta}-glucan-induced trained immunity modulates monocyte differentiation to ameliorate experimental colitis, highlighting the potential of harnessing trained immunity as a therapeutic strategy to recalibrate innate immune responses and restore gut homeostasis in IBD, shedding light for future clinical applications. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=189 SRC="FIGDIR/small/653036v2_ufig1.gif" ALT="Figure 1"> View larger version (56K): org.highwire.dtl.DTLVardef@1b969c2org.highwire.dtl.DTLVardef@1ce603dorg.highwire.dtl.DTLVardef@10582forg.highwire.dtl.DTLVardef@10d7de6_HPS_FORMAT_FIGEXP M_FIG C_FIG

immunology↗

bioRxiv2025

Inhibiting glucocorticoid receptors enhances adult spinal cord neural stem cell activity and improves outcomes in spinal cord injury

The internal microenvironment plays a critical role in the proliferation and differentiation of endogenous neural stem/progenitor cells (NSPCs). A big change in the spinal cord injury (SCI) microenvironment is the elevated level of glucocorticoids. In this study, we examined the impact of glucocorticoids on endogenous NSPCs in the adult mouse spinal cord. Our findings reveal that adult spinal cord NSPCs express glucocorticoid receptors, but not mineralocorticoid receptors. Glucocorticoids were found to significantly inhibit the proliferation and neurosphere formation of NSPCs via activation of glucocorticoid receptors, and they also impaired their differentiation. Importantly, the glucocorticoid receptor inhibitor CORT125281 was shown to enhance motor function in a traumatic SCI model in mice. Treatment with CORT125281 increased the number of NSPCs at the injury site in vivo. Flow cytometry and RNA sequencing analyses indicated that glucocorticoids induce NSPC arrest in the G1/G0 phase through the p53 signaling pathway. Glucocorticoids increased the expression of cell-cycle regulatory genes p15, p16, p18, and p27 in adult spinal cord NSPCs. In summary, our data suggest that glucocorticoids elevation following SCI suppresses the proliferation of endogenous NSPCs via glucocorticoid receptor activation. Targeting glucocorticoid receptors with specific inhibitors may represent a novel therapeutic strategy to promote recovery after spinal cord injury.

neuroscience↗

bioRxiv2025

Beyond Natural Antibodies: Scaffold-Based Generation of Novel Anti-3CLpro Nanobody Nb01

In the post-pandemic era, continuous mutations and persistent infections of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) pose a significant threat to global health, making the normalization of preventive measures imperative. Due to its high conservation, the 3CLpro is relatively stable across all these variants without significant changes, suggesting that drugs targeting this enzyme could be effective against all variant viruses. And compared to traditional antibodies, nanobodies show significant advantages against SARS-CoV-2 and its variants. Traditional antibodies often lose their inhibitory activity due to viral mutation. Nanobodies are characterised by their small size, high stability, high affinity for antigen binding, and high water solubility, which enable them to capture viruses quickly and effectively address the continuous mutations and persistent infections of SARS-CoV-2. In this research, we devised a strategy to produce nanobodies by utilizing a fragment-generating large language model, resulting in the identification of a nanobody named Nb01. Nb01 exhibits potent and broad-spectrum neutralizing activity against numerous SARS-CoV-2 variants. The nanobody Nb01, directed against the SARS-CoV-2 3CLpro, demonstrated efficacy against the majority of prevalent SARS-CoV-2 variants. Notably, it has a higher affinity than the current best performing nanobodies (S43, bn03, R14, and 3-2A2-4) for most of the variants, including the Alpha (27.5%), Gamma (29.7%), Omicron BA.2 (32.2%), BA.4/5 (81.2%), BF.7 (64.2%) and XBB (5.5%) variants. For other variants, Nb01 displayed affinities that were on par with these benchmark nanobodies. In summary, the exceptional specificity, low toxicity, robust stability, and extensive spectrum of Nb01 indicate its potential to be developed as a nanobody therapeutic for the management of SARS-CoV-2 infections and its diverse variants.

bioinformatics↗

bioRxiv2025

Anks3 mediates cilia dependent polycystin signaling and is essential for adult kidney homeostasis

The existence of a cilia-dependent cyst activation (CDCA) pathway underlying autosomal dominant polycystic kidney disease was identified by showing that cyst progression following loss of polycystins is significantly suppressed by removal of structurally intact cilia. We applied translating ribosome affinity purification RNASeq on pre-cystic mouse kidneys to determine a cell-autonomous in vivo translatome associated with CDCA and identified Glis2 as an early effector of polycystin signaling. Here, to discover additional components of CDCA, we used polycystin-dependent Glis2 expression as a functional readout and identified Anks3, from the CDCA pattern translatome, as a candidate cytosolic regulator of polycystin signaling. Anks3 regulates polycystin-dependent Glis2 expression both in vitro and in vivo. Anks3 also undergoes polycystin-dependent changes in phosphorylation state. Inactivation of Anks3 in Pkd1 mouse models suppresses cyst progression, but also results in rapidly progressive kidney injury independent of polycystins. Anks3 inactivation also normalizes a broader spectrum of polycystin-dependent CDCA translatome changes. These findings define Anks3 as a central regulator of cilia dependent polycystin signaling, functioning downstream of cilia and polycystins and upstream of Glis2, and show that Anks3 has broader functions in maintaining renal structural and functional homeostasis.

genetics↗

bioRxiv2025

Ancient DNA Reveals Hominoid Evolution: Intermediate DNA Sequences and Advances in Molecular Paleontology

AbstractFossils and ancient crude pottery vessels function as physical "DNA containers," preserving oriDNA (original, in situ DNA) and accumulating eDNA (environmental DNA) over time. Ancient DNA (aDNA) serves as molecular fossils, chronicling evolutionaryhistory. Using "nano-affinitybead technology", we extracted and sequenced DNAfrom Lycoptera fossils in the Jehol region and a "round-bellied jar (Jar)" from the Erlitou period in Guangwu Town, yielding 236,545 primate sequences from the fossils and 86,908 from the pottery. We observed that the AFF value of DNA sequences negatively corre lates with species divergence time1, offering a quantitative measure of DNA preservation and host divergence. Some fragments distinct from modern genomic sequences, termed "intermediate DNAsequences" (IDS), have been identified. Many IDS exhibit an upper age limit, preserving characteristics of the last common ancestor (LCA) of the Hominidae and offering molecular insights into "Darwins puzzle". Among IDS, the SRRA subtype (Sequence Reversal and Rearrangement), identified in mRNA-coding exonic sequences, arises from the incorporation of a complementary antisense strand upstream of the sense strand, either adjacent to it or separated bya sequence interval. This introduces a novel post-transcriptional regulatory mechanism at the mRNA level, driven by SRRA, which presets hairpin structures and Indels in the UTR or CDS of exonic sequences, modulating gene variation. We propose: "SRRAs played a critical trial-and-error role in early Hominidae evolution, facilitating adaptive genomic changes, with some SRRA sequences later excised from exons", positioning SRRAas an evolutionary "genetic switch". Additionally, seven species -specific fragments (SSFs) of non-human primates (NHPs) linked to Asian Homo erectus were identified in the fossils, and pottery DNA reveale d sequences from tropical species (e.g., zebrass, oil palms), providing evidence of climate-driven local extinction and supporting paleo-ecological and paleo-environmental reconstruction. This method of analyzing aDNA from non-skeletal materials opens new avenues in paleontology, archaeology, and geology, guiding the tracing of ancient migration patterns and fossil searches. DNAfragments preserved within "DNA containers " exhibit an "old-few, new-many" turnover pattern, with many aDNA fragments displaying non-deamination. This evidence challenges prevailing perspectives, the authenticity criteria for aDNA, and the capabilities and scope of the traditional research method, necessitating a thorough reevaluation of the relevant knowledge framework. Furthermore, this study opens new opportunities for frontier research.

paleontology↗

bioRxiv2025

SIMIT-seq: a bead-free, scalable microfluidic platform for single cell mRNA sequencing with ultrahigh cell-indexing rate

SIMIT-seq is a bead-free, scalable microfluidic platform designed for high-efficiency single-cell mRNA sequencing. Conventional microfluidic-based single-cell RNA sequencing platforms rely heavily on barcoded beads and intricate co-encapsulation schemes, often constrained by double Poisson limitations and the complexities of bead synthesis. In contrast, SIMIT-seq eliminates the need for beads entirely by employing a deterministic, orthogonal barcoding strategy within a two-dimensional micro-well array. This platform achieves an impressive single-cell indexing rate of 96.6% without the need for complex microfluidic operations. Here, we describe the design and fabrication of the SIMIT-seq platform, outline its workflow for transcript capture and library preparation, and demonstrate its application in profiling K562 cells. Our results validate both the high fidelity of molecular barcode immobilization and the systems capability to support downstream single-cell mRNA sequencing. SIMIT-seq offers a cost-effective and scalable alternative for single-cell transcriptomics, providing a promising foundation for future single-cell omics applications.

bioinformatics↗

bioRxiv2025

Expanding the chicken gut virome: Uncovering viral diversity, host interactions, and regional variations across the intestinal tract

Chicken gastrointestinal virome comprises a complex and diverse viral community with significant implications for host health and microbiome function. We analyzed 3,312 publicly available chicken gut metagenomic datasets to establish the chicken gastrointestinal virome collection (CGVD), which includes 39,380 non-redundant viral operational taxonomic units (vOTUs); notably, 84.90% (33,433/39,380) represent novel sequences absent from current databases. Over half of the CGVD vOTUs were classified as bacteriophages, predominantly from the order Caudovirales. The predicted hosts were mainly prokaryotes, particularly Bacillota and Bacteroidota, revealing a multifaceted landscape of virus-host interactions. Many vOTUs infected multiple bacterial phyla, indicating high adaptability and broad ecological impact. In addition, lifestyle prediction showed that 28.28% (11,137 /39,380) of the vOTUs in CGVD were identified as lytic phages. Functional annotation demonstrated that viral genes contribute to key metabolic processes, including nucleotide and amino acid metabolism, thereby facilitating viral replication and host adaptation. The detection of auxiliary metabolic genes and carbohydrate-active enzymes underscores the role of viruses in modulating the gut microbiome. Although antibiotic resistance genes and mobile genetic elements were present, their contribution to horizontal gene transfer appears limited. Additionally, marked regional differences in virome composition were observed between the small and large intestines, particularly in the abundance of families such as Siphoviridae and Myoviridae. CGVD not only highlights the key role of viruses in shaping the chicken gut microbiome and influencing microbial dynamics and metabolic pathways, but also provides new resources and insights for future research.

microbiology↗

bioRxiv2025

Tissue-wide profiling of human lungs reveals spatial sequestration of macrophages in tuberculosis

The immune response to human tuberculosis (TB), particularly in the context of complex lung pathology, remains incompletely understood. Here, we employed whole-slide spatial proteomics to map immune cell organization in TB-affected human lung tissues. Our analysis revealed pronounced spatial segregation of major immune cell populations in non-necrotizing TB lesions. At the tissue level, macrophages and lymphocytes formed distinct cellular communities associated with specific pathological features. At the lesion level, macrophages and B cells showed an inverse relationship in both abundance and spatial distribution. Proinflammatory T cells preferentially accumulated in macrophage-rich lesions but remained largely separated from macrophages. Interestingly, lesions exhibiting clear segregation between T cells and macrophages were more common in subclinical TB than in active disease. These findings suggest that spatial isolation of macrophages from effector lymphocytes may help temper inflammation and potentially prevent lesion progression to necrosis, while also enabling immune evasion by Mycobacterium tuberculosis. One Sentence SummaryXiao et al. reveal spatial segregation of immune cells in TB-lung tissue and link the microenvironmental dynamics to disease states of tuberculosis.

immunology↗

bioRxiv2025

A ketogenic diet mitigates hippocampal astrogliosis in epileptic brain

The ketogenic diet (KD) is an established treatment for patients with medically intractable epilepsy and is chiefly characterized by high fat/low-carbohydrate intake and the production of ketone bodies (KB) such as {beta}-hydroxybutyrate (BHB). However, after more than a century of clinical use, the mechanisms underlying its efficacy remain unclear. While prior investigations have examined the effects of the KD and its metabolic substrates on synaptic transmission, few studies have explored a potential connection between astrocytic ion channels and seizure genesis. One essential function of astrocytes is spatial potassium buffering which influences passive potassium conductance (PPC), and when impaired, can result in neuronal hyperexcitability. In the present study, we demonstrate that the KD can mitigate hippocampal astrogliosis in the Kcna1-null (KO) mouse model of developmental epilepsy. Specifically, we observed a significant increase in GFAP expression in KO mice fed a control diet compared to wild-type (WT) mice, and that the KD prevented this change. Furthermore, we noted a reduction in hippocampal astrocytic PPC in epileptic mice, whereas KD-treated KO animals exhibited nearly normal passive conductance levels. In this regard, we found that while Kir4.1, TREK-1 and TWIK-1 RNA expression levels were not significantly altered by KD treatment in either WT or KO mice, BHB appeared to only minimally affect Kir4.1-mediated currents in transfected HEK cells. Furthermore, bulk RNA-seq analysis of the various treatment groups revealed KD-induced down-regulation of factors linked to hippocampal astrogliosis. Our findings indicate that the KD protects against epilepsy-associated astrogliosis and astrocytic PPC changes, underscoring a novel mechanism of action, and implicate extracellular potassium in its anti-seizure effects.

neuroscience↗

bioRxiv2025

High-Quality Cell Capture Reveals Transcriptomic Changes After Single-Axon Injury of Mauthner Cells

In vivo single-cell capture methods based on micropipettes are essential for correlating morphological characteristics with transcriptomic profiling under physiological conditions. However, they often suffer from significant contamination of off-target cells. Consequently, we developed Hip-seq, which significantly reduces heavily contaminated cells, decreases contamination levels, improves cell reproducibility, and enhances data analysis accuracy compared to patch-seq. Using Hip-seq, we found that axon regeneration failure could be due to abnormal activation of translation and the circadian clock. Axon-regenerable central neurons reactivated axon development-related genes during regeneration. And one-to-one associated analysis helped identify pro-regenerative genes.

neuroscience↗

bioRxiv2025

Phase separation drives SNARE complexes formation

BackgroundNeuronal exocytosis is mainly driven by the assembly of the soluble N-ethylmaleimide-sensitive factor attachment protein receptor (SNARE) complexes. However, little is known about the organization principle of the SNARE complex. MethodsProtein condensates formed by SNARE complex were imaged by confocal microscope. Fluorescence recovery after photobleaching (FRAP) assay together with fusion and division assays at the cellular level and in vitro studies with purified proteins were performed to characterize the dynamic properties of protein condensates. The effect of SNARE complex phase separation on the recruitment of synaptic vesicles was detected by immunofluorescence. ResultsWe discover that phase separation drives SNARE complex formation and aggregation; in addition, nonintrinsically disordered regions (non-IDRs) of the syntaxin1 protein is necessary for the formation of these biological condensates. Functionally, phase separation of the SNARE complex can be regulated by the major cofactors of the fusion machinery and has the ability to recruit synaptic vesicles in neurons. ConclusionsOur study here establishes that phase separation is a promising way to mediate the formation and aggregation of the SNARE complex, and further identified that the non-IDRs of syntaxin1 is necessary for the phase separation of the SNARE complex. Our work answers an vital scientific question: does the SNARE complex function as multiple copies that are dispersed or clustered together to ensure sustained neurotransmitter release. In sum, phase separation provides an ideal working model for SNARE complex-mediated membrane fusion and neurotransmitter release.

neuroscience↗

bioRxiv2025

Unveiling Protein-DNA Interdependency: Harnessing Unified Multimodal Sequence Modeling, Understanding and Generation

The interdependent orchestration of proteins, coding DNA sequences (CDS), and adjacent regulatory DNA elements underpins biological functionality, where evolutionary constraints shape codon usage, transcriptional regulation, and structural stability. We present ProDMM, a multimodal framework that deciphers these systemic relationships through unified sequence modeling. Integrating a context-aware encoder with conditional generation, our architecture captures codependent patterns between protein motifs and cis-regulatory syntax. ProDMMs encoder demonstrates superior predictive capabilities in forecasting pathway-level phenotypes and protein expression profiles, outperforming conventional single-modality approaches. Its decoder generates synthetically optimized regulatory elements by resolving spatial dependencies between coding sequences and adjacent non-coding regions, enabling transcriptional fine-tuning unavailable to sequence-agnostic methods. By resolving how localized CDS-NCDS-protein interdependencies propagate to system-level phenotypes, ProDMM establishes a paradigm for holistic biological sequence engineering. This approach enables coordinated optimization of translation efficiency, enzymatic activity, and pathway flux, offering transformative potential for designing tailored biosynthesis systems and advancing sustainable bioproduction strategies.

bioinformatics↗