Biology subjects

Hu, N.

Publications and source records attributed to Hu, N..

At least 19 recordsLinked to original sources

bioRxiv2026

Phagocytic activity of perivascular cell promotes CNS injury pathology

Injury, stroke, and neurological diseases cause persistent accumulation of cellular debris that deteriorates lesion microenvironment and impedes central nervous system (CNS) repair. Debris clearance in the injured CNS has long been attributed primarily to microglia and infiltrating macrophages. Here, we identify perivascular cells as previously unrecognized phagocytes that expand after injury and exhibit robust phagocytic activity. Perivascular cell phagocytosis is conserved across multiple mouse models of CNS injury and human stroke lesions. These cells exhibit key hallmarks of phagocytosis, including LC3-associated phagocytosis for efficient lysosomal degradation. Mechanistically, phosphatidylserine serves as the eat-me signal and Axl mediates myelin debris uptake. Myelin phagocytosis drives perivascular cell proliferation, fibrosis and lesion progression. Genetic deletion of Axl in perivascular cells or pharmacological inhibition with the FDA-approved Axl inhibitor Gilteritinib reduces pathology and improves functional recovery after spinal cord injury. Together, these findings establish Axl-dependent perivascular cell phagocytosis as a therapeutic target for CNS repair.

neuroscience↗

bioRxiv2026

A dish-to-biobank framework links β-cell nutrient-stress programs to genetic and dietary risk for Type 2 Diabetes

Type 2 diabetes (T2D) arises from genetic susceptibility and chronic metabolic stress, but whether these converge on shared molecular programs in human populations remains unclear. Here, we develop a dish-to-biobank framework linking controlled {beta}-cell perturbation to population-scale disease genetics through the circulating plasma proteome, and apply it to T2D. scRNA-seq of human stem cell-derived islets under factorial glucose and palmitate exposure identifies their combination (glucolipotoxicity) as the condition eliciting the strongest SC-{beta} cell transcriptional response, with glucolipotoxicity-upregulated genes uniquely enriched for T2D heritability, monogenic diabetes genes, and rare-variant burden signals. CRISPR knockout of {beta}-cell identity regulators PAX6 and PDX1 aligns with this program, establishing convergence of environmental and genetic perturbations on a shared disease-relevant state. We then used the plasma proteome as an accessible population-scale readout of these experimentally defined {beta}-cell stress programs, scoring 45,956 UK Biobank White British participants. We define heritable stress signatures that associate with refined carbohydrate and saturated fat intake, and undergo trans-tissue genetic regulation, with a subset of variants showing diet-dependent effects. Together, these findings establish glucolipotoxicity as a genetically anchored model of {beta}-cell dysfunction and provide a generalizable framework for linking controlled cellular perturbations to human disease genetics at population scale.

genetics↗

bioRxiv2026

Lineage tracing and live-cell imaging reveal that NeuroD1 does not reprogram microglia into neurons

In situ glia-to-neuron conversion induced by a single transcription factor is a promising regenerative strategy for treating central nervous system injuries and neurodegenerative diseases. Previous studies reported that NeuroD1 can induce microglia-to-neuron cross-lineage conversion and improve recovery after brain injury. However, these findings remain controversial. To examine the ability of NeuroD1 in inducing microglia-to- neurons conversion, we employed virus-free genetic lineage tracing systems to specifically induce NeuroD1 expression in microglia, and track the cell fate of NeuroD1-expressing cells at multiple timepoints. Meanwhile, we longitudinally monitored NeuroD1-expressing microglia via two-photon imaging, and characterized their transcriptional profile by single-cell RNA sequencing. All observations across these methods revealed that NeuroD1-expressing cells retained their microglia identity, and cannot convert into neurons, no matter under physical and injury conditions. Instead, sustained expression of NeuroD1 facilitated microglia apoptosis in vivo. Collectively, our findings provide strong evidence that NeuroD1 alone is sufficient to induce microglia-to neuron conversion. This study further highlighted the importance of rigorous lineage-tracing and cell fate mapping strategies for validating in situ glia-to-neuron conversion.

neuroscience↗

bioRxiv2026

Neural coupling between spinal motor neurons of the first dorsal interosseous muscle during individual index finger flexion and pinch tasks

ObjectivePrecision grip tasks require complex coordination of intrinsic hand muscles, yet how common synaptic inputs to motor neurons are modulated during functionally different tasks remain unclear. This study investigated whether neural coupling between motor unit spike trains in the first dorsal interosseous (FDI) muscle differs between isolated index finger flexion and precision pinch tasks. ApproachSixteen healthy participants performed isolated index finger flexion and pinch tasks at 10% and 20% of maximal voluntary contraction while high-density surface electromyography was recorded from the FDI. Motor unit spike trains were decomposed and tracked across tasks. Neural coupling was assessed using complementary methods: coherence analysis and Proportion of Common Input (PCI) index to quantify linear common oscillations in delta (1-5 Hz), alpha (5-15 Hz), and beta (15-35 Hz) frequency bands, and mutual information-based network analysis to capture nonlinear interactions. Main results.Coherence analysis and PCI revealed no significant differences between tasks across all frequency bands. In contrast, network density derived from mutual information analysis showed significantly stronger nonlinear motor unit coupling during pinch compared to isolated finger flexion (p = 0.013), independent of force level. Significance.These findings demonstrate a dissociation between linear and nonlinear measures of motor unit coupling. In particular, precision pinch tasks appear to rely on stronger higher-order common inputs and distinct neural control strategies that are not fully captured by traditional linear coherence measures. This highlights that functionally relevant precision behaviors engage additional layers of nonlinear neural coupling, offering new insight into how the nervous system adaptively modulates motor unit coordination to meet complex task demands.

neuroscience↗

bioRxiv2026

pertTF: context-aware AI modeling for genome-scale and cross-system perturbation prediction

Predicting genetic perturbation responses at a single-cell level is central to building models for cell state and disease. However, existing approaches are limited on predicting phenotypic outcomes beyond expression changes and generalizing predictions across genome-scale perturbations in biologically relevant contexts. Here we introduce pertTF, a transformer-based single-cell genetic perturbation model. pertTF was trained from a unique dataset capturing single cell expressions profiles of 30 full gene knockouts across 14 relevant cell types during human pancreatic development and beta-cell differentiation. pertTF outperforms current methods in predicting expression changes of perturbing unseen genes in unseen cellular contexts. In addition, pertTF infers perturbation-induced shifts in cell identity and population composition, an important phenotypic outcome of perturbation in many physiology and disease settings. Through transfer learning, pertTF operates in physiologically relevant systems, including primary human islets, where large-scale perturbation experiments are challenging. The generalizability of pertTF is further demonstrated by in silico pooled and single-cell CRISPR screens, capturing critical regulators of stem cells and early pancreatic cell development. These results establish pertTF as a framework for integrating large-scale single-cell perturbation data with AI models to predict genetic perturbation effects across cellular systems and disease contexts.

bioinformatics↗

bioRxiv2026

SPrOUT: A computational and targeted sequencing approach for mixed plant DNA identification with Angiosperms353

PremiseThe identification of plant species from mixed samples is crucial in various fields, including ecological surveys, conservation efforts, and food and dietary supplement safety. Traditional methods face potential challenges due to the high costs of DNA sequencing, inefficiencies in computational workflows, and incomplete sequence databases. Methods and ResultsThis study introduces a novel approach using the Angiosperms353 target sequencing kit for efficient taxonomic identification of angiosperm DNA in mixed samples. Our method assembles short pair-end reads for each mixed sample. Using gene sets of Angiosperms353 from 871 species, we apply phylogenetic inference to categorize the variance in phylogenetic distance across genes to identify the presence of taxa in mixed plant samples. The pipeline reaches 98.1 to 99.6% accuracy, 92.9 to 100% precision for identifying unknown taxa in in-silico mixes, and 90.7% accuracy and 98.0% precision for mock supplement mixtures. We explored the parameter cutoffs of the pipeline to offer an empirical range for different applications. ConclusionsThe Angiosperms353 and HybPiper assembly proved effective in sorting mixed plant DNA samples. Our method offers a framework for scientific and practical applications in plant species identification in both single and mixed samples.

bioinformatics↗

bioRxiv2025

A stem cell knockout village reveals lineage rewiring and a non-canonical islet cell fate in monogenic diabetes

Genetics studies have identified a core set of regulators essential for pancreatic {beta} cell development, many of which are mutated in monogenic diabetes. However, how these mutations alter developmental trajectories to produce pathological cell states remains elusive. Here we introduce a knockout village framework that enables longitudinal scRNA-seq profiling of 79 human pluripotent stem cell mutant lines targeting 30 developmental regulators, including 15 diabetes genes, across five islet differentiation stages. We show that loss of lineage regulators impairs {beta} cell formation in a stage-specific manner and rewires developmental trajectories towards competing lineages. Notably, several monogenic diabetes gene mutations drive a shift from {beta} cells to enterochromaffin (EC)-like cells, a recently recognized non-canonical islet cell fate. These EC-like cells exhibit incomplete activation of hormone regulation programs, along with elevated neuron signatures. Leveraging the diversity of cell fate outcomes across mutants, we predicted and experimentally validated ISL1 as a key downstream effector of PDX1 and PAX6 that safeguards {beta} cell identity against an EC-like fate. Together, our findings reveal cell fate rewiring as a widespread, previously underappreciated pathological mechanism in monogenic diabetes and establish a scalable platform for uncovering developmental vulnerabilities in human genetic disorders.

developmental biology↗

bioRxiv2025

Motor unit rate coding in intrinsic hand muscles during isolated finger contractions and pinch task

PurposeMuscle force output is modulated via motor unit recruitment and rate coding, yet how rate coding in intrinsic hand muscles differs between isolated and synergistic hand tasks remains unclear. This study examined motor unit discharge behaviour in the first dorsal interosseous (FDI) and thenar during isolated index finger flexion, isolated thumb flexion, and a tip pinch task. MethodsSeventeen participants performed each task at 10%, 20%, and 30% of their maximal voluntary contraction (MVC) while high-density surface electromyograms (HDsEMG) were recorded from both muscles. Motor unit spike trains were completely decomposed from the HDsEMG recordings, tracked across force levels, and their mean discharge rates and recruitment thresholds were calculated. ResultsFor both FDI and thenar muscles, the mean discharge rate increased with force, but the FDI exhibited steeper slopes than the thenar and at 10-20% MVC than 20%-30% MVC. In addition, lower recruitment thresholds and higher mean discharge rates were observed in the FDI compared to the thenar. Task-dependent differences were also observed in the FDI, with the pinch task yielding higher discharge rates than isolated contractions. In the thenar, differences between tasks were limited to higher forces. ConclusionThese findings demonstrate muscle- and task-specific motor unit modulation across forces in the intrinsic hand muscles, where the FDI relies more on rate coding, while the thenar likely prioritizes recruitment to cope with increased force demands.

physiology↗

bioRxiv2025

A novel enterococcus phage endolysin Lys22 with a wide host range against mixed biofilm of Enterococcus faecalis, Staphylococcus aureus and Acinetobacter baumannii

The global surge in multidrug-resistant (MDR) bacterial pathogens has created an urgent imperative for innovative antimicrobial strategies. Enterococcus faecalis, Staphylococcus aureus, and Acinetobacter baumannii demonstrate remarkable antibiotic resistance and dominate hospital-acquired infections. These bacteria often form biofilms, a complex community structure that shields them from immune system phagocytosis, resists antibiotic penetration, and enhances their survival in harsh environments. In clinical cases, these bacteria often form mixed biofilms and lead to treatment failures. Phages and their derivatives have emerged as promising candidates in the fight against drug-resistant bacteria. Lys22, an endolysin derived from an enterococcus phage, has been cloned and demonstrated to possess a broad host range, effectively targeting E. faecalis, various Staphylococcus species, and A. baumannii. When applied to the biofilms formed by these bacteria, Lys22 was found to significantly inhibit both simple and complex biofilms in vitro. Virulent genes, including agrA, sarA, and icaA in S. aureus; asa1, cylA, and hyl in E. faecalis; and OmpA and lpsB in A. baumannii were also downregulated by Lys22. Notably, Lys22 also exhibited a robust protective effect against dual or triple infections involving E. faecalis, S. aureus, and A. baumannii in a zebrafish eggs model, highlighting its potential as a therapeutic agent in combatting multi-bacterial infections.

microbiology↗

bioRxiv2024

H3K27M diffuse midline glioma is homologous recombination defective and sensitized to radiotherapy and NK cell-mediated antitumor immunity by PARP inhibition

BackgroundRadiotherapy (RT) is the primary treatment for diffuse midline glioma (DMG), a lethal pediatric malignancy defined by histone H3 lysine 27-to-methionine (H3K27M) mutation. Based on the loss of H3K27 trimethylation producing broad epigenomic alterations, we hypothesized that H3K27M causes a functional double-strand break (DSB) repair defect that could be leveraged therapeutically with PARP inhibitor and RT for selective radiosensitization and antitumor immune responses. MethodsH3K27M isogenic DMG cells and orthotopic brainstem DMG tumors in immune deficient and syngeneic, immune competent mice were used to evaluate the efficacy and mechanisms of PARP1/2 inhibition by olaparib or PARP1 inhibition by AZD9574 with concurrent RT. ResultsH3K27M mutation caused an HRR defect characterized by impaired RT-induced K63-linked polyubiquitination of histone H1 and inhibition of HRR protein recruitment. H3K27M DMG cells were selectively radiosensitized by olaparib in comparison to isogenic controls, and this effect translated to efficacy in H3K27M orthotopic brainstem tumors. Olaparib and RT induced an innate immune response and induction of NK cell (NKG2D) activating ligands leading to increased NK cell-mediated lysis of DMG tumor cells. In immunocompetent syngeneic orthotopic DMG tumors, either olaparib or AZD9574 in combination with RT enhanced intratumoral NK cell infiltration and activity in association with NK cell-mediated therapeutic responses and favorable activity of AZD9574. ConclusionsThe HRR deficiency in H3K27M DMG can be therapeutically leveraged with PARP inhibitors to radiosensitize and induce an NK cell-mediated antitumor immune response selectively in H3K27M DMG, supporting the clinical investigation of best-in-class PARP inhibitors with RT in DMG patients. Key pointsO_LIH3K27M DMG are HRR defective and selectively radiosensitized by PARP inhibitor. C_LIO_LIPARP inhibitor with RT enhances NKG2D ligand expression and NK cell-mediated lysis. C_LIO_LINK cells are required for the therapeutic efficacy of PARP inhibitor and RT. C_LI Importance of the StudyRadiotherapy is the cornerstone of H3K27M-mutant diffuse midline glioma treatment, but almost all patients succumb to tumor recurrence with poor overall survival, underscoring the need for RT-based precision combination therapy. Here, we reveal HRR deficiency as an H3K27M-mediated vulnerability and identify a novel mechanism linking impaired RT-induced histone H1 polyubiquitination and the subsequent RNF168/BRCA1/RAD51 recruitment in H3K27M DMG. This model is supported by selective radiosensitization of H3K27M DMG by PARP inhibitor. Notably, the combination treatment results in NKG2D ligand expression that confers susceptibility to NK cell killing in H3K27M DMG. We also show that the novel brain penetrant, PARP1-selective inhibitor AZD9574 compares favorably to olaparib when combined with RT, prolonging survival in a syngeneic orthotopic model of H3K27M DMG. This study highlights the ability of PARP1 inhibition to radiosensitize and induce an NK cell-mediated antitumor immunity in H3K27M DMG and supports future clinical investigation.

cancer biology↗

bioRxiv2024

A vacuolar invertase gene SlVI modulates sugar metabolism and postharvest fruit quality and resistance in tomato

Sugars act as signaling molecules to modulate various growth processes and enhance plant tolerance to various abiotic and biotic stresses. Moreover, sugars contribute to the post-harvest flavor in fleshy fruit crops. To date, the regulation of sugar metabolism and its effect in plant growth, fruit ripening, postharvest quality and resistance remains not fully understood. In this study, we investigated the role of tomato gene encoding a vacuolar invertase, hydrolyzing sucrose to glucose and fructose. SlVI is specifically expressed during the tomato fruit ripening process. We found that overexpression of SlVI resulted in increased leaf size and early flowering, while knockout of SlVI led to increased fruit sucrose content, enhanced fruit firmness, elevated resistance of postharvest fruit to Botrytis cinerea. Moreover, the content of naringenin and total soluble solids was significantly increased in SlVI knockout fruit at postharvest stage. Transcriptome analysis showed a negative feedback regulation triggered by sucrose accumulation in SlVI knockout fruit resulting in a downregulation of BAM3 and AMY2, which are critical for starch degradation. Moreover, genes associated with cell wall, cutin, wax, and flavonoid biosynthesis and pathogen resistance were upregulated in SlVI knockout fruit. Conversely, the expression levels of genes involved in cell wall degradation were decreased in knockout fruit. These results are consistent with the enhanced postharvest quality and resistance. Our findings not only provide new insights into the relationship between tomato fruit sucrose content and postharvest fruit quality, but also suggest new strategies to enhance fruit quality and extend postharvest shelf life.

plant biology↗

bioRxiv2024

FADS and semi-rational design modified T7 RNA polymerase reduced dsRNA production, with lower terminal transferase and RDRP activities

T7 RNA polymerase (T7 RNAP) is the preferred tool for in vitro transcription (IVT), it synthesizes mRNA while accompanied by the generation of dsRNA by-products. This undesirable dsRNA triggers immune stress responses, compromises therapeutic efficacy, and raises safety concerns. To evolve T7 RNAP for reduced dsRNA, we pursued two complementary strategies. Firstly, the FADS (fluorescence-activated droplet sorting) based on molecular beacons was used to screen random libraries with diversity exceeding 105. Secondly, we constructed several single-site saturated libraries to facilitate the transition of T7 RNAP from the initiation to the elongation conformation. These libraries were screened using the traditional microplate-based dual-probe screening technique. Both approaches identified two dominant variants: Mut1 (V214A) and Mut7 (F162S/A247T) from FADS, Mut11 (K180E) and Mut14 (A70Q) from saturated libraries. Furthermore, the combinatorial mutant Mut17 (A70Q/F162S/K180E), generated via DNA shuffling, exhibited significantly reduced dsRNA production compared to the wild-type under various conditions, ranging from 0.18% to 1.80%, with a minimum value of 0.5 pg/g. Cell experiments confirmed that variants generated capped-mRNA with similar quality and quantity to the wild-type, while significantly reducing immune stress response in cells. These results indicate the compatibility and broad potential applications of these mutations. We then observed a close correlation between the production of dsRNA and the activities of T7 RNAP in terminal transferase and RDRP. Particularly, the terminal transferase activity appears to play a critical role in dsRNA generation. These findings align with the mechanism of dsRNA formation during IVT and provide new screening criteria for further evolution of T7 RNAP.

molecular biology↗

bioRxiv2023

Reproductive sexual dimorphisms in two willow species, Salix exigua Nutt. and S. nigra Marshall.

Premise of the ResearchThe prevalence of sexual dimorphisms, which evolve due to contrasting strategies to maximize reproductive success in males and females, is variable among dioecious plant species. In the Salicaceae, many traits have been assessed across many studies, but direct or indirect associations between these traits and reproductive allocation are often neglected. Given the dynamic evolution of sex determination systems and the strong interest in wood production in the family, we wondered whether sexual dimorphisms related to reproduction may have gone unreported. Here, we assess sexual dimorphism in reproductive traits in two species of Salix. Recognition of reproductive sexually dimorphic traits will contribute to understanding the evolution of sex determination systems in the Salicaceae. MethodologyWe conducted observational studies in natural populations to assess the presence of sexual dimorphisms in early spring bud density, catkin number, and flower number per catkin across four sampling periods in Salix exigua. We also analyzed flower number and catkin number per flower in Salix nigra. Pivotal ResultsWe observed no sexual dimorphism in pre-season buds per branch in S. exigua but did find that males produced more flowers per catkin and more catkins per branch than females in both S. exigua and S. nigra. ConclusionsHigher flower numbers in males compared to females is consistent with expectations from intra-sexual selection among males. The presence of reproductive sexual dimorphisms in Salix suggests that sexual selection may affect the evolution of mating strategies in Salix species, and the evolution of the sex determination system within this genus.

plant biology↗

bioRxiv2023

Comparison between Canine and Porcine Models of Chronic Deep Venous Thrombosis

Venous thromboembolism(VTE) refers to deep venous thrombosis(DVT) and pulmonary embolism(PE), which is a worldwide problem and has very high morbidity and mortality. The research of venous thrombosis involves pathogenesis, pathophysiology, and therapeutic attempt. Alternative experimental animal models have changed dramatically over the past 20 years, from small murine models to large ones. Larger animal models offer more options and are more consistent with human physiology. This article aims to induce chronic deep venous thrombosis in the left iliac vein in canine and porcine models and compare these two models. We think that feasible large animal models can better translate the results of therapeutic research into clinical application.

animal behavior and cognition↗

bioRxiv2023

Phylogenomics reveals patterns of ancient hybridization and differential diversification contributing to phylogenetic conflict in Populus L. and Salix L.

Despite the economic, ecological, and scientific importance of the genera Populus L. (poplars, cottonwoods, and aspens) and Salix L. Salicaceae (willows), we know little about the sources of differences in species diversity between the genera and of the phylogenetic conflict that often confounds estimating phylogenetic trees. Salix subgenera and sections, in particular, have been difficult to classify, with one recent attempt termed a spectacular failure due to a speculated radiation of the subgenera Vetrix and Chamaetia. Here we use targeted sequence capture to understand the evolutionary history of this portion of the Salicaceae plant family. Our phylogenetic hypothesis was based on 787 gene regions and identified extensive phylogenetic conflict among genes. Our analysis supported some previously described subgeneric relationships and confirmed polyphyly of others. Using an fbranch analysis we identified several cases of hybridization in deep branches of the phylogeny, which likely contributed to discordance among gene trees. In addition, we identified a rapid increase in diversification rate near the origination of the Vetrix-Chamaetia clade in Salix. This region of the tree coincided with several nodes that lacked strong statistical support, indicating a possible increase in incomplete lineage sorting due to rapid diversification. The extraordinary level of both recent and ancient hybridization in both Populus and Salix have played important roles in the diversification and diversity in these two genera. Supplementary data files will be provided by request to matt.olson@ttu.edu

evolutionary biology↗

bioRxiv2022

Mutated cells mediate distinct inflammatory responses in clonal hematopoiesis

Clonal hematopoiesis (CH) is an age-associated phenomenon that increases risk for hematologic malignancy and cardiovascular disease. CH is thought to enhance disease risk through inflammation in the peripheral blood1. Here, we profile peripheral blood gene expression in 66,968 single cells from a cohort of 17 CH patients and 7 controls. Using a novel mitochondrial DNA barcoding approach, we were able to identify and separately compare mutant TET2 and DNMT3A cells to non-mutant counterparts. We discovered the vast majority of mutated cells were in the myeloid compartment. Additionally, patients harboring DNMT3A and TET2 CH mutations possessed a pro-inflammatory profile in CD14+ monocytes through previously unrecognized pathways such as galectin and macrophage Inhibitory Factor (MIF). We also found that T cells from CH patients, though mostly un-mutated, had decreased expression of GTPase of the immunity associated protein (GIMAP) genes, which are critical to T cell development, suggesting that CH may impair T cell function. Key points- CD14+ monocytes from clonal hematopoiesis patients stimulate inflammation through increased cytokine expression. - T cells from clonal hematopoiesis are deficient in GIMAP expression, suggesting CH may impair T cell differentiation.

genetics↗

bioRxiv2022

QCR7 affects the virulence of Candida albicans and the uptake of multiple carbon sources present in different host niches

BackgroundCandida albicans is a commensal yeast that may cause life-threatening infections. Studies have shown that the cytochrome b-c1 complex subunit 7 gene (QCR7) of C. albicans encodes a protein that forms a component of the mitochondrial electron transport chain complex III, making it an important target for studying the virulence of this yeast. However, to the best of our knowledge, the functions of QCR7 have not yet been characterized. MethodsA QCR7 knockout strain was constructed using SN152, and BALb/c mice were used as model animals to determine the role of QCR7 in the virulence of C. albicans. Subsequently, the effects of QCR7 on mitochondrial functions and use of carbon sources were investigated. Next, its mutant biofilm formation and hyphal growth maintenance were compared with those of the wild type. Furthermore, the transcriptome of the qcr7{Delta}/{Delta} mutant was compared with that of the WT strain to explore pathogenic mechanisms. ResultsDefective QCR7 attenuated the virulence of C. albicans infection in vivo. Furthermore, the mutant influenced the use of multiple alternative carbon sources that exist in several host niches. Moreover, it led to mitochondrial dysfunction. Furthermore, the QCR7 knockout strain showed defects in biofilm formation or the maintenance of filamentous growth. The overexpression of cell-surface-associated genes (HWP1, YWP1, XOG1, and SAP6) can restore defective virulence phenotypes and the carbon-source utilization of qcr7{Delta}/{Delta}. ConclusionThis study provides new insights into the mitochondria-based metabolism of C. albicans, accounting for its virulence and the use of variable carbon sources that promote C. albicans to colonize host niches.

microbiology↗

bioRxiv2022

CRIC-seq reveals positional rule of PTBP1-mediated long-range RNA looping in splicing regulation

RNA-binding proteins bind at different positions of pre-mRNA molecules to promote or reduce the usage of a particular exon. Seeking to understand the working principle of these positional effects, we develop a CRIC-seq method to enrich single RBP-mediated in situ RNA-RNA spatial interacting fragments for deep sequencing. We determine hnRNPA1- and PTBP1-mediated RNA-RNA interactions and regulatory mechanisms in HeLa cells. Unexpectedly, 3D RNA map analysis shows that PTBP1-mediated loops in introns preferably promote cassette exon splicing by accelerating asymmetric intron removal, whereas the loops spanning across cassette exon primarily repress splicing. This "positional rule" can faithfully predict PTBP1-regulated splicing outcomes. We further demonstrate that cancer-related splicing quantitative trait loci can disrupt RNA loops by reducing PTBP1 binding on pre-mRNAs to cause aberrant splicing in tumors. Our study presents a powerful method for exploring the functions of RBP-mediated RNA-RNA interactions in gene regulation and disease.

molecular biology↗