Biology subjects

Yang, Y.

Publications and source records attributed to Yang, Y..

At least 433 records · Page 24Linked to original sources

bioRxiv2025

DICAR-JP Regulates Ribosome Migration, a New Theory of Mitochondrial Protein Production

BackgroundDICAR plays a cardioprotection of diabetic models. DICAR-JP, a short sequence of DICAR, may represent DICARs active functional domain. NAC is necessary for the heart tissue development. Addtionally, OGDHL is a metabolism regulator. In this study, we examine a new mechanism of DICAR via NAC/OGDHL on regulating cardiomyocyte metabolism in DCM. We also sought to elucidate the function of DICAR/DICAR-JP in modulating NAC-dependent production of OGDHL nascent peptides and their mitochondrial translocation, and we also aimed to optimize the DICAR-JP sequence to be better therapy on DCM. MethodsSPR was to investigate the binding interaction between DICAR-JP and NAC. The function of DICAR-JP and DICAR-JP45 on OGDHL nascent peptide transfection was detected by in vitro translation approach. Biotin-DICAR-JP was transfected to study the function of DICAR-JP, NAC and OGDHL. Untargeted metabolomics was utilized to characterize the metabolic reprogramming of cardiomyocytes. AAV9-DICAR-JP and DICAR-JP45 were constructed and administered to db/db mice for 1-2 months to assess their cardioprotective effects detected by Echocardiography confirmed mouse cardiac function. ResultsOur findings demonstrated that DICAR-JP be the functional domain that interacts with NAC to regulate OGDHL nascent peptide expression. Disruption of OGDHL expression reversed the metabolic reprogramming observed in diabetic cardiomyocytes, highlighting its crucial role in maintaining cardiac metabolic homeostasis. DICAR-JP facilitated the translocation of OGDHL nascent peptides from the cytoplasm to the mitochondria, leading us to hypothesize that DICAR-JP plays a key role in regulating ribosomal migration from the endoplasmic reticulum to the mitochondria. We refer to this process as the Ribosome Migration. In our studies using AAV9-mediated DICAR-JP and DICAR-JP45 overexpression in heart tissue. DICAR-JP and DICAR-JP45 both exhibited significant cardioprotective effects against diabetic cardiomyopathy (DCM), comparable to those observed with Empagliflozin. ConclusionsIn a conclusion, we propose a new endogenous nucleic acid candidate drug library, and a new molecular framework, the Ribosome Migration, which implicates the DICAR-JP/NAC/OGDHL nascent peptide axis in metabolic reprogramming related to DCM. This theory constructs a new mitochondrion protein from nuclear original protein. Moreover, DICAR-JP45 shows strong potential as a nucleic acid-based therapeutic candidate for treating DCM. Novelty and SignificanceO_ST_ABSWhat Is Known?C_ST_ABSDICAR is a new protective circular noncoding RNA for diabetic cardiomyopathy. NAC is located in ribosome and regulates new peptide production, which is also a key factor in heart tissue development. OGDHL can regulate different energy metabolism in mitochondria. What New Information Does This Article Contribute?DICAR-JP is the functional domain that interacts with NAC to regulate OGDHL nascent peptide expression. There is an interaction between DICAR-JP and NAC. DICAR-JP sequence is protected by NAC and NAC function is mediated by DICAR-JP. We called this RNA functional domain. OGDHL expression reversed the metabolic reprogramming observed in diabetic cardiomyocytes, highlighting its crucial role in maintaining cardiac metabolic homeostasis. DICAR-JP takes part in tanscription and translocation of OGDHL nascent peptides from the cytoplasm to the mitochondria via plasma ribosome. We call this process the Ribosome Migration Theory. DICAR-JP and DICAR-JP45 both exhibited significant cardioprotective effects against diabetic cardiomyopathy (DCM), comparable to those observed with Dapagliflozin (DAPA). Our study revealed a novel molecular framework, the Ribosome Migration Theory, which implicates the DICAR-JP/NAC/OGDHL nascent peptide axis in metabolic reprogramming related to DCM. Moreover, DICAR-JP45 shows strong potential as a nucleic acid-based therapeutic candidate for treating DCM.

pharmacology and toxicology↗

bioRxiv2025

RBMX2: A Pivotal Regulator Linking Mycobacterium bovis Infection to Epithelial-Mesenchymal Transition and Lung Cancer Progression

Tuberculosis (TB) is a complex disease that arises from the dynamic interplay among the pathogen, host, and environmental factors. In 2022, TB affected approximately 10.6 million people worldwide, resulting in 1.3 million deaths. In regions with a high burden of zoonotic TB, Mycobacterium bovis (M. bovis) accounts for nearly 10% of human TB cases. The immune evasion strategies and latent nature of Mycobacterium tuberculosis (M. tb) pose significant challenges to understanding the host immune response to TB infection. In this study, we identify RNA-binding motif protein X-linked 2 (RBMX2) as a novel host factor that may facilitate M. bovis infection. However, the molecular mechanisms and functional roles of RBMX2 during M. bovis infection remain poorly understood. Our findings show that RBMX2 is significantly upregulated across multiple cell types following infection, including embryonic bovine lung (EBL) cells, bovine macrophage (BoMac) cells, bovine pulmonary alveolar primary cells, and human alveolar epithelial cells (A549). Using a combination of global transcriptomic sequencing, proteomic profiling, cell adhesion assays, ChIP-PCR, and Western blotting, we demonstrate that RBMX2 suppresses cell adhesion and tight junction formation in EBL cells while promoting M. bovis adhesion and invasion through activation of the p65 signaling pathway. Importantly, integrated analyses of transcriptomic, proteomic, and metabolomic data reveal that RBMX2 plays a key role in regulating epithelial-mesenchymal transition (EMT), a cellular process closely associated with cancer progression. To further explore the potential link between RBMX2 and cancer, we analyzed the TIMER2.0 database and found elevated RBMX2 expression in lung adenocarcinoma (LUAD) and lung squamous cell carcinoma (LUSC) tissues compared to normal lung tissues. These findings were corroborated by immunofluorescence staining. Using an M. bovis-infected BoMac-induced EBL-EMT model, we show that RBMX2 promotes EMT through activation of the p65/MMP-9 pathway following infection. Additionally, we validated the EMT process in human lung epithelial cancer cells (H1299), further supporting the involvement of RBMX2 in this transition. Collectively, our study identifies RBMX2 as a novel host factor that may enhance M. bovis infection and drive infection-induced EMT. These findings provide new insights into the molecular mechanisms underlying TB pathogenesis and suggest that RBMX2 could serve as a potential target for the development of TB vaccines and therapeutic strategies against TB-associated lung cancer.

microbiology↗

bioRxiv2025

Cooperation Between Genotoxic Bacteria Accelerates Tumorigenesis in a Mouse Model of Colon Carcinogenesis

To identify causal links between gut microbes and tumorigenesis, we colonized groups of germ-free colon tumor-susceptible mice (ApcMin/+;Il10-/-) with 15 cultured human fecal microbiotas from healthy individuals, as well as patients with inflammatory bowel disease and colorectal cancer. The number of colonic tumors in ApcMin/+;Il10-/- mice varied by donor microbiota but not by the health status of the donor. In vitro screens of host cell proliferation, genotoxicity, and inflammation in bacteria-mammalian cell cocultures revealed that genotoxicity best predicted tumorigenic microbes in vivo with genotoxic microbes present in all tested individuals. The genotoxic subset of strains from each donor induced more tumors than the complete community - even when the complete community was not tumorigenic. Combining genotoxic microbes from multiple sources increased tumor number and decreased the time to tumor onset. Together these results suggest that most individuals harbor genotoxic bacterial strains and the balance of genotoxic to protective strains determines the timing and severity of tumorigenesis in vivo.

microbiology↗

bioRxiv2025

TRPV1 Defends the Healthy Murine Cornea against Staphylococcus aureus Adhesion Independently of Sensory Nerve Firing

PurposePreviously we showed that transient receptor potential ion channels TRPA1 and TRPV1 selectively protect the cornea against bacterial adhesion, with TRPA1 countering the Gram-negative pathogen Pseudomonas aeruginosa and TRPV1 countering environmental bacteria. Here, we explored parameters of this specificity using a Gram-positive pathogen Staphylococcus aureus. MethodsHealthy corneas of C57BL/6J wild-type (WT), TRPA1 (-/-) or TRPV1 (-/-) mice were challenged with S. aureus for 4 or 6 hours. Some experiments instead/also used resiniferatoxin (RTX) to deplete TRPV1-expressing nerves, JNJ-17203212 to selectively antagonize TRPV1, or the anesthetic bupivacaine to inhibit nerve firing. Adherent bacteria were quantified using FISH labeling (16S rRNA-targeted probe). Lyz2+, CD11c+ and CD45+ cells were visualized/quantified using hybrid mT/mG + LysMcre mice (red cell membranes; Lyz2+-GFP), CD11c+-YFP mice, and anti-CD45-antibody respectively. ResultsCorneas of TRPV1 (-/-) not TRPA1 (-/-) mice were found more susceptible to S. aureus adhesion compared to WT. Accordingly, either ablation of TRPV1-expressing nerves or TRPV1 antagonism increased adhesion. Defense against S. aureus adhesion did not depend on nerve firing. Despite having no significant impact on CD11c+ or Lyz2+ cell numbers, S. aureus challenge increased CD45+ cell counts, also dependent on TRPV1-expressing nerves, and it increased Lyz2+ cell sphericity and volume. ConclusionHealthy corneas utilize TRPV1 to protect against S. aureus adhesion independently of sensory nerve firing. This contrasts with defense against P. aeruginosa adhesion which requires TRPA1 and nerve firing. How the differential immune cell responses to these two pathogens relate to TRP-dependent defense against adhesion remains to be determined.

microbiology↗

bioRxiv2025

Palmdelphin facilitates R-spondin2 secretion to activate Wnt signaling and promote colorectal cancer stemness and tumorigenesis

The Wnt signaling pathway is a key driver of stemness and progression which contributes to mortality in colorectal cancer (CRC). R-spondins bind to LGR receptors to inhibit ubiquitin E3 ligases, thus protecting Frizzled from degradation and activating downstream Wnt signaling. Herein, we identify Palmdelphin (PALMD) as a functional marker of CRC stem cells, interspersed between intestinal and colonic crypt base epithelial cells, and predictive of aggressive CMS4 CRC and poor survival. Gene knockdown and overexpression studies revealed that PALMD initiates paracrine activation of Wnt/{beta}-catenin signaling via interacting with and facilitating the secretion of R-spondin2 (RSPO2), resulting in enhanced stemness and tumor growth in vitro and in vivo. Physiologic or pharmacologic inhibition of the PALMD-RSPO2 axis using R-spondin2-specific antibody or 6-methyl-1,3,8-trihydroxyanthraquinone (emodin), respectively, attenuates PALMD- mediated Wnt reporter activation, self-renewal, and tumorigenesis in cell and patient-derived organoid models. Together, these findings identify PALMD as a previously unknown player in Wnt signaling in CRC, and underscore the pro-tumorigenic role of R-spondin2 in this context.

cancer biology↗

bioRxiv2025

Capturing Natural Evolution in Function-guided RNA Design via Genomic Foundation Models

RNAs play critical roles in gene expression regulation, catalysis, genetic information transmission, and immune response. However, current RNA engineering approaches face limitations in designing RNA for efficient in vivo folding and functional execution. Here, we present a novel, zero-shot strategy that integrates genomic large language models (LLMs) with inverse folding models (IFMs) to generate RNA sequences that mirror natural evolutionary patterns while preserving the structural integrity of critical functional regions. Benchmarking 9 state-of-the-art genomic foundation models, we show that their unsupervised log-likelihood scores correlate strongly with RNA fitness, enabling zero-shot sequence design. Applied to fluorescent RNA aptamers, our approach yielded 20 Broccoli variants, over half of which achieved up to 155% in fluorescence and a twofold increase in binding affinity, with robust performance both in vitro and in vivo. For Pepper, two rounds of optimization produced 40 variants, 16 of which demonstrated up to 2.6 fold in fluorescence and a threefold boost in binding affinity, including five with superior in vivo brightness.This approach offers a scalable, efficient, and resource-light method for RNA design, with significant implications for RNA-based therapeutics and diagnostics. By leveraging general foundation models to facilitate RNA evolution in a zero-shot fashion, we believe our work represents a major advancement in the field of RNA engineering.

evolutionary biology↗

bioRxiv2025

Hepatic Yap1 activates systemic catabolism and muscle loss during organ repair: evidence for a liver-derived common mechanism with cancer cachexia.

Recovery from critical injury concomitant with restoration of functional organ mass invokes a systemic catabolic response leading to muscle and fat loss, known as cachexia. We interrogated this process using mouse models of organ repair, including liver regeneration after hepatectomy, Yap1-mediated hepatomegaly, and pneumonectomy. Both hepatectomy and Yap1 induced systemic catabolism. Muscle and adipose wasting scaled with degree of liver growth, with 10-25% reduction of muscle mass and 50-80% of fat mass. In contrast, non-regenerative lung injury did not induce tissue wasting. Liver growth elevated resting energy expenditure. Tracer studies demonstrated redistribution of muscle-derived cholesterol and amino acids to regenerating liver. Gene expression changes in livers and muscles showed high concordance between the liver growth models and cancer cachexia models, including pancreatic adenocarcinoma cachexia. We propose that cachexia is a normal and essential reparative process in organ repair and regeneration and further, that cancer cachexia is a pathological exacerbation of an adaptive process mediated by activation of Yap1 in the liver.

physiology↗

bioRxiv2025

Lymphatic Malformations with Activating KRAS Mutations Impair Lymphatic Valve Development Through Matrix Metalloproteinases

BACKGROUNDLymphatic malformations (LMs) are lesions due to inherited or somatic mutations that lead to a defective lymphatic vasculature. Activating KRAS mutations have been identified recently in LM patients with lymphedema, chylous ascites, or life-threatening chylothorax. In a LM mouse model, KRAS mutations are associated with a loss of lymphatic valves, which has been proposed to cause chylothorax via retrograde lymph flow into the pleural space. However, the mechanisms underlying the loss of lymphatic valves are unknown. METHODSTo investigate the mechanisms leading to valve loss, we combined the lymphatic-specific and tamoxifen-inducible Flt4CreERT2 with Kras-loxP-stop-loxP-G12D (Kras+/G12D) mice and Prox1GFP reporter mice to induce the restricted expression of KRAS-G12D and enable valve quantification in postnatal pups. Human dermal lymphatic endothelial cells (hdLECs) expressing KRAS-G12D were probed for changes in mRNA and protein expression with qRT-PCR, western blot, and gel zymography, and mechanistic studies were performed using 3D cell culture in collagen matrices. RESULTSOur data showed that lymphatic-specific expression of KRAS-G12D significantly attenuated valve development in the mesentery, diaphragm, and ear skin. qRT-PCR, western blot, and gel zymography using hdLECs expressing KRAS-G12D revealed the upregulation of the plasminogen activator (PA) pathway and matrix metalloproteinases (MMPs). The MMPs were sufficiently activated by plasmin, the product of the PA pathway, in hdLECs grown in a 3D collagen matrix, indicating a role for MMPs in the degradation of valve ECM core. Furthermore, a broad-spectrum MMP inhibitor given to Flt4CreERT2;Kras+/G12D mice rescued lymphatic valve development. CONCLUSIONSWe conclude that hyperactive KRAS signaling upregulates MMPs that become excessively activated by the upregulation of the PA pathway. MMPs then degrade the lymphatic valve ECM core preventing valve formation.

pathology↗

bioRxiv2025

Validation of diverse and previously untraceable Sendai virus copyback viral genomes by Direct RNA Sequencing

Copyback viral genomes (cbVGs) are truncated viral genomes with complementary ends produced when the viral negative-sense RNA virus polymerase detaches from the replication template and resumes elongation from the nascent strand. Despite advances in methods to identify cbVGs based on the site of polymerase break and rejoin, PCR-based tools cannot provide full length sequences of most cbVGs and/or can introduce errors and artifacts during cbVG amplification. These limitations have painted a limited picture of the diverse population of cbVGs generated during infection. To improve our ability to obtain native full-length sequences of cbVGs, we optimized Direct RNA Sequencing (DRS) as a fast and simple tool to sequence full-length cbVGs and designed a BLAST-based analysis approach to identify cbVGs from long-read sequencing data. We analyzed the DRS outputs of multiple Sendai virus stocks to highlight both the utility and limitations of this tool. We found that to capture the dominant 546 nucleotide cbVG produced by Sendai virus strain Cantell, the length of complementarity between the virus trailer and the DRS oligonucleotide should optimally be increased to up to 32 nucleotides. We also demonstrate comparable quality of cbVG sequences by DRS from as little RNA as 17.6ng from the media fraction or 50ng of from the cellular fraction of cells infected with SeV, in contrast to the recommended 1000ng. Importantly, we validated different cbVG species from two recombinant Sendai virus stocks, including for the first time cbVGs whose break positions occurred at or near position one in the reference genome. ImportanceMost viruses of the order Mononegavirales has been demonstrated to naturally generate copyback viral genomes. These genomes are critical determinants of infection outcomes; they interfere with standard virus replication by competing for viral resources, activate antiviral responses, and inhibit protein translation. Despite their critical roles in infection, current tools to study copyback viral genomes rely either on preexisting knowledge of the sequence of a target RNA or require reverse-transcription and amplification of the target RNA, biasing toward short cbVGs and introducing relatively high rates of errors. Our lab has long advocated for RNA virologists to sequence their stocks to assess the role cbVGs may have in their infections. Toward this effort, we detail the optimization of Direct RNA Sequencing to sequence full-length cbVGs while maintaining the integrity of the native cbVG RNA and present the Long-Read cbVG Analysis (LoCA; https://github.com/lopezlab-washu/LOCA.git) script as a highly accessible BLAST-based tool for cbVG detection.

microbiology↗

bioRxiv2025

Expression spectrum of TE-derived transcripts in human adult tissues

Transposable elements (TEs) are vital components of eukaryotic genomes and have played a critical role in genome evolution. Although most TEs are silenced in the mammalian genome, increasing evidence suggests that certain TEs are actively involved in gene regulation during early developmental stages. However, the extent to which human TEs drive gene transcription in adult tissues remains largely unexplored. In this study, we systematically analyzed 17,329 human transcriptomes to investigate how TEs influence gene transcription across 47 adult tissues. Our findings reveal that TE-derived transcripts are broadly expressed in human tissues, contributing to both housekeeping functions and tissue-specific gene regulation. We identified sex-specific expression of TE-derived transcripts regulated by sex hormones in breast tissue between females and males. Our results demonstrated that TE-derived alternative transcription initiation significantly enhances the variety of translated protein products, e.g., changes in the N-terminal peptide length of WNT2B caused by TE-derived transcription result in isoform-specific subcellular localization. Additionally, we identified 68 human-specific TE-derived transcripts associated with metabolic processes and environmental adaptation. Together, these findings highlight the pivotal evolutionary role of TEs in shaping the human transcriptome, demonstrating how conserved and human-specific TEs contribute to transcriptional and translational innovation in human genome evolution.

genomics↗

bioRxiv2025

A Telomere-to-Telomere Diploid Reference Genome and Centromere Structure of the Chinese Quartet

Recent advances in sequencing technologies have enabled the complete assembly of human genomes from telomere to telomere (T2T), resolving previously inaccessible regions such as centromeres and segmental duplications. Here, we present an updated, higher-quality, haplotype-phased T2T assembly of the Chinese Quartet (T2T-CQ), a family cohort comprising monozygotic twins and their parents, generated using high-coverage ONT ultralong and PacBio HiFi sequencing. The T2T-CQ assembly serves as a crucial reference genome for integrating publicly available multi-omics data and advances the utility of the Quartet reference materials. The T2T-CQ assembly scores highly on multiple metrics of continuity and completeness, with Genome Continuity Inspector (GCI) scores of 77.76 (maternal) and 76.41 (paternal), quality values (QV) > 70, and Clipping Reveals Assembly Quality (CRAQ) scores > 99.6 for both haplotypes, enabling complete annotation of centromeric regions. Within these regions, we identified novel 13-mer higher-order repeat patterns on chromosome 17 which exhibited a monophyletic origin and emerged approximately 230 thousand years ago. Overall, this work establishes an essential genomic resource for the Han Chinese population and advances the development of a T2T pan-Chinese reference genome, which will significantly enable future investigations both into population-specific structural variants and the evolutionary dynamics of centromeres.

genomics↗

bioRxiv2025

Field Survey of Anopheles Mosquito and Their Culturable Gut Bacteria in the Border Regions of Yunnan Province, China

Despite the elimination of domestic malaria transmission within China, the border areas of Yunnan Province continue to face a heightened risk of imported cases due to the presence of diverse Anopheles mosquito species and the widespread burden of malaria in neighboring countries. While the mosquito gut microbiota offers a promising avenue for developing anti-malaria strategies, a meticulous investigation of the various Anopheles species and their associated gut microbiota in Yunnans border areas has yet to be undertaken. To address this gap, field surveys were conducted over the years 2020, 2021, and 2023. These surveys resulted in the collection of a substantial sample comprising 4,221 adult female mosquitoes spanning sixteen species with Anopheles sinensis identified as the predominant species. Furthermore, 741 cultivable strains of gut symbiotic bacteria were isolated and classified into four phyla comprising 109 genera with the composition of dominant bacteria varying annually. This study provides valuable insights into the population dynamics of malaria vectors in the border regions of Yunnan province, China, along with the intestinal bacteria they harbor including several bacterial species which exhibit promising anti-plasmodium effects. By leveraging the antagonistic effects of symbiotic bacteria against Plasmodium, our findings contribute to an ongoing global endeavor to develop innovative Anopheles management and malaria prevention strategies.

microbiology↗

bioRxiv2025

A new class of OLD family ATPases functions in cell cycle progression in thermoacidophilic archaea

Overcoming lysogenization defect (OLD) proteins are diverse ATPases-nucleases functioning in antiphage defense in bacteria. However, the role of these proteins in archaea is currently unknown. Here, we describe a new class of archaeal OLD family ATPases and show that they do not appear to be involved in antiviral defense but play an essential role in cell cycle progression. The gene in Saccharolobus islandicus REY15A, named as Cran1 (Cell cycle related ATPase and nickase 1), cannot be deleted and exhibits cyclic expression patterns, with a peak expression during the transition from M-G1 to S cell cycle phase. Cran1 overexpression leads to significant growth retardation, cell size enlargement, and increased cellular DNA content. Cran1 displays potent nickase and ATPase activities in vitro, with the nickase activity being dependent on the presence of the ATPase domain. Notably, Cran1 copurifies with chromatin-associated proteins, such as Cren7 and a histone deacetylase homolog, suggesting its involvement in chromatin-related activities. Collectively our results suggest that Cran1 plays an important role in cell cycle progression, revealing a novel function of OLD family proteins.

microbiology↗

bioRxiv2025

A Rapid and Highly Sensitive CRISPR Assay Utilizing Cas12a Orthologs for the Detection of Novel Duck Reovirus

The novel duck reovirus (NDRV) disease presents a significant threat to the poultry industry due to the absence of effective therapeutic measures. As a result, there is an urgent need to develop innovative rapid diagnostic methods for early virus detection. In this study, we developed a Rapid Visual CRISPR Assay to detect the NDRV S3 gene using novel Cas12a orthologs. Specifically, we compared the performance of two candidates, Gs12-16 and Gs12-18, in detecting the NDRV S3 gene to identify a highly sensitive and efficient CRISPR-based diagnostic method. Our results demonstrated that both Gs12-16 and Gs12-18 exhibited strong cis- and trans-cleavage activities for classical "TTTV" protospacer adjacent motif (PAM)-containing targets in vitro, although they required different reaction temperatures. Notably, Gs12-18 showed relatively higher activity for dsDNA targets compared to Gs12-16, indicating that Gs12-18 is more suitable for CRISPR-based nucleic acid detection applications. To leverage these properties, we integrated Gs12-18 with loop-mediated isothermal amplification (LAMP) technology to establish a LAMP-CRISPR/Gs12-18-mediated method for detecting the NDRV S3 gene. This approach enables highly sensitive and visually detectable on-site identification of the NDRV S3 gene, achieving a sensitivity of 38 copies per reaction. Our LAMP-CRISPR/Gs12-18-based method can be utilized for highly sensitive detection of NDRV nucleic acids.

synthetic biology↗

bioRxiv2025

Construction of Complete Telomere-to-Telomere Genome Assembly of the Rabbit Using Haploid Embryonic Stem Cells

The rabbit owns commercial importance in meat and fur production, and also has long served as a valuable animal model in biomedical research. Yet, the complete assembly of a high-quality rabbit reference genome has not been established. Here, we present a telomere-to-telomere (T2T) genome assembly of the New Zealand White (NZW) rabbit, the most complete and accurate rabbit genome to date. Using a haploid embryonic stem cells (haESCs) to overcame the challenges of homologous sequence interference and structural variation, we generate a genome with a contig N50 of 137.71 Mb, anchoring all chromosomes with only three gaps, through integrating long-read sequencing (PacBio HiFi, Oxford Nanopore), Hi-C, and Illumina data. Quality assessments reveal near-complete coverage of the BUSCO mammalian gene set, with 99.61% completeness. Notably, this complete assembly allowed for the first comprehensive annotation of the rabbit immunoglobulin loci and major histocompatibility complex region, which were previously unresolved in earlier genome versions. The NZW-T2T assembly based on haESCs not only provides a critical resource for advancing rabbit-based research, but also set a new benchmark for de novo genome assembly for other animals with complex genome.

genomics↗

bioRxiv2025

Roles and transcriptional regulation of the endogenous cellulases in association with substrate and cellular processes in a thermoacidophilic archaeon

Microbes of the order Sulfolobales are potentially next generation platforms for cellulose degradation and utilization. However, the mechanisms of cellulose degradation and utilization remain unclear. In this study, we analyzed the enzymatic activity, localization, transcriptional regulation, and interplay of three endogenous cellulases Cel1, Cel2A, and LacS, and the association of transcription with cellular processes in the model thermophilic archaeon Saccharolobus islandicus REY15A. Overexpression strains based on a vector developed in this study as well as single and double deletion mutants of the three cellulase genes were constructed and analyzed. We reveal that Cel1 and Cel2A are membrane-associated, and a higher proportion of Cel2A is secreted into the medium than Cel1. The expression of all the three cellulases is induced by carboxymethylcellulose sodium (CMC). Furthermore, we found that the transcriptional levels of cel1, cel2A, and lacS are interdependent and cel1 and cel2A levels apparently increased with lacS deletion and overexpression of an ABC transporter, suggesting of an intracellular oligosaccharide-dependent regulatory mechanism. We showed that a cell cycle transcription factor aCcr1 binds to the promoter of cel1 in vitro. Additionally, we accidentally found that the cellulase genes expression increases in the presence of uracil synthesis pathway and deletion of the cellulase genes facilitates cell growth in CMC-containing medium. This study reveals an ingenious and intricated mechanism for cellulose utilization to adapt to extreme environment in archaea and provide insights for engineering Sulfolobales archaea as biomass-degrading and utilization platforms.

microbiology↗

bioRxiv2025

AIPAMPDS: an AI platform for antimicrobial peptide design and screening

Antimicrobial resistance (AMR) presents a pressing global health crisis, particularly in the post-pandemic era, underscoring the urgent need for innovative therapeutics. Antimicrobial peptides (AMPs) hold promises for combating multidrug-resistant infections but are hindered by challenges in clinical translation, including limited hemocompatibility and inefficient design processes. To overcome these obstacles, we developed AIPAMPDS, an AI-driven computational platform that integrates a deep generative model with multi-stage screening to design highly active, non-haemolytic AMPs. The platform features two key modules: (1) a Generative Pre-trained Transformer (GPT)-based framework for target-specific AMP generation, enabling rapid exploration of novel peptide sequences, and (2) a multi-neural network screening pipeline for dual evaluation of antimicrobial activity and toxicity. By systematically evaluating both AI-generated and natural candidate AMPs, we identified ten lead peptides for experimental validation, of which 90% exhibited negligible haemolytic activity while maintaining robust antimicrobial potency. AIPAMPDS bridges computational design and therapeutic application, significantly advancing AMP discovery and providing a powerful tool for next-generation antimicrobial development. The platform is freely accessible via a web server at https://amps.pianlab.cn/AIPAMPDS/. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=94 SRC="FIGDIR/small/644774v1_ufig1.gif" ALT="Figure 1"> View larger version (35K): org.highwire.dtl.DTLVardef@14e9a20org.highwire.dtl.DTLVardef@168e811org.highwire.dtl.DTLVardef@5bd9beorg.highwire.dtl.DTLVardef@344c34_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioinformatics↗

bioRxiv2025

Pcdh20 is a POU2F3 target gene required for proper tuft cell microvillus formation

BACKGROUND & AIMSTuft cells play protective roles in infection, inflammation, and tumorigenesis through the secretion of cytokines and eicosanoids. Tuft cells are known for their tall, blunt microvilli, thought to be analogous to mechanosensory hair cell stereocilia; however, a functional role for the microvillar apparatus has not been identified. POU2F3 is the master regulator transcription factor for tuft cells, yet how POU2F3 drives formation of this unique structure is unknown. Here, we aimed to identify POU2F3 target genes and commonalities between tuft and hair cells to better understand this unique structure. METHODSPOU2F3 ChIP-seq was performed on tuft cells and compared to the hair cell transcriptome. Tuft cell RNA-seq datasets were interrogated for hair cell structural and mechanosensory genes; expression was validated. Intestinal and gallbladder tuft cells were examined using multiple light and electron microscopy (EM) modalities. PCDH20 was knocked down in mouse models and ultrastructural analyses were performed. The tuft cell cytoskeleton was modeled using AlphaFold3 prediction. RESULTSGenes encoding structural and mechanosensory proteins common to both tuft and hair cells, including Pcdh20, were identified. Imaging localized PCDH20 to tuft cell microvilli and hair cell stereocilia. Genetic ablation of Pcdh20 in mice resulted in structural defects in tuft cell microvilli, including loss of rigidity and organization. Molecular modeling suggests PCDH20 homodimers link adjacent microvilli. CONCLUSIONSPcdh20 is a POU2F3 target gene in tuft cells, critical to maintain the rigid microvillar apparatus. These findings, together with the shared expression of mechanosensory components like TMC1, support the hypothesis that tuft cells could have mechanosensory capabilities analogous to cochlear hair cells.

cell biology↗