Biology subjects

Tian, M.

Publications and source records attributed to Tian, M..

At least 19 recordsLinked to original sources

bioRxiv2026

Asymmetric Boost Responses to an HIV-1 Vaccine: Boost-site Controls Secondary B-cell Fates

Induction of broadly neutralizing antibody (bnAb) responses remains a central challenge to designing efficacious HIV vaccines. Lineage design strategies, in which bnAb precursors are guided via iterative immunizations to their mature forms, depend on high levels of somatic mutation and the recall of antigen-specific B cells. Recent studies have identified spatial context as an important determinant of boosting efficacy, but the application of this to HIV vaccines and the underlying mechanisms are incompletely understood. Here, using mice harboring a V3-glycan bnAb lineage precursor knock-in combined with lineage-tracing and single-cell analyses, we show that persistent germinal centers (GCs) support continued affinity maturation of founder clones and ipsilateral boosting preferentially engages these lineages in secondary GCs. In contrast, contralateral boosting predominantly recruits naive B cells and memory B cells not directed towards the immunizing antigen. The few memory cells recruited at this site were biased towards a plasma cell fate. Finally, we identify disfavored mutational trajectories within the V3-glycan bnAb lineage, revealing intrinsic constraints on bnAb lineage evolution.

immunology↗

bioRxiv2026

B Cell Receptor Signaling Sets Boundaries for Selection of Broadly Neutralizing Antibody Functional Mutations

B cell signaling is required for germinal center (GC) selection and synergizes with T cell-help leading to differentiation into effector cells and a protective antibody response. Here, we studied the relationship between B cell signaling and the selection of functional mutations in a humanized mouse model of a CD4 binding-site specific HIV-1 broadly neutralizing antibody precursor. While BCR signaling increased with antigen affinity, immunization-induced frequency of a functional mutation was inversely related to affinity and favored a gain in association rate. Antigen-specific GC B cells and key mutation frequency were higher in the mid-affinity (0.5 - 5M) than in either the higher or lower affinity group, and were consistent with the significantly higher serum neutralization titers in the mid-range group. Our studies show that BCR signaling imposes boundaries (upper/lower) for selection of antibody functional mutations and support a "Goldilocks Zone" model that defines the favored BCR signaling strength for GC selection.

immunology↗

bioRxiv2026

Quantitative profiling of intrinsic dCas9-DNA recognition reveals key determinants of guide RNA performance

CRISPR technologies based on nuclease-deactivated Cas9 (dCas9) rely on programmable DNA binding rather than DNA cleavage, yet the intrinsic DNA-recognition properties that govern optimal guide RNA (gRNA) performance remain poorly understood. Existing approaches either measure genomic occupancy in cells or infer dCas9 behavior from cleavage-based Cas9 datasets, despite DNA binding being substantially more permissive than DNA cleavage. Here we introduce TANGO (Targeted Array-based Nucleic acid-Guided Occupancy), a high-density DNA-array platform that quantitatively profiles intrinsic dCas9:gRNA binding across tens of thousands of DNA targets in a cell-free system. TANGO captures established features of dCas9 target recognition, while providing substantially greater sensitivity than prior assays. Comparison with ChIP-seq data demonstrates that intrinsic DNA-binding specificity is a major driver of genomic occupancy and reveals that chromatin accessibility modulates the intrinsic binding affinity required for dCas9 recruitment. Across CRISPRi/a guides, TANGO identifies multiple independent biochemical determinants of guide performance--including on-target affinity, mismatch tolerance, and ribonucleoprotein assembly--and flags problematic and highly promiscuous guides overlooked by current specificity metrics. Unexpectedly, some guides retain substantial guide-directed DNA binding even in the absence of a protospacer-adjacent motif (PAM), revealing an additional dimension of dCas9 specificity. Together, these results establish intrinsic DNA recognition as a quantitative and experimentally accessible determinant of dCas9 function, providing a framework for improving guide selection and enhancing the precision of CRISPR technologies.

genomics↗

bioRxiv2026

Phytophthora cinnamomi populations collected from avocado in the United States exhibit high adaptive capacity to climate and disease control methods

Phytophthora cinnamomi, the causal agent of Phytophthora root rot (PRR), poses a persistent threat to the United States avocado industry, the top domestic producer and consumer. Avocado growers are facing clonal A2 P. cinnamomi populations challenging their current PRR control methods. In this study, we characterized 125 isolates collected from orchards in California, Florida, Hawaii, Texas, and Puerto Rico for radial growth per day, optimal growth temperature, in vitro fungicide sensitivity, and virulence on DAnjou pear fruit and UC2001 avocado seedlings. Across all isolates, optimal growth occurred most frequently at a range from 22 to 25{degrees}C; however, a subset of isolates from Hawaii, Florida, and California exhibited higher optimal growth temperatures (28{degrees}C and 30{degrees}C) suggesting thermal adaptation in warmer regions. Potassium phosphite EC50 values spanned from 4.61 to 763.13 {micro}g/ml, with significantly higher insensitivity in isolates from California and Florida, reflecting the continued overuse of this fungicide in these major production states. In contrast, baseline sensitivities to ethaboxam, mandipropamid, mefenoxam, fluopicolide, and oxathiapiprolin were uniformly high, with narrow, unimodal EC50 distributions across states. Finally, a wide range of virulence among isolates was detected using avocado seedlings and DAnjou pear fruits with isolates from California and Puerto Rico being the most virulent. Together, this data documents extensive phenotypic diversity within clonal A2 P. cinnamomi populations including heat-adapted and phosphite-insensitive lineages, establishes multi-state fungicide sensitivity baselines, and underscores the need for continued surveillance, integrated fungicide stewardship (especially phosphonates), and rootstock screening against phenotypically diverse populations to sustain avocado PRR management and ensure the United States avocado industry sustainability and profitability.

microbiology↗

bioRxiv2026

Isolation of folate-producing probiotics and its regulatory effects on homocysteine metabolism and gut microbiota composition

BackgroundFolate deficiency is a global nutritional problem associated with multiple adverse health outcomes, including impaired one-carbon metabolism and elevated homocysteine levels (hyperhomocysteinemia). Gut microbiota-mediated folate biosynthesis has emerged as a promising strategy for improving host folate status. This study aimed to isolate folate-producing probiotic strains, clarify their folate synthesis mechanisms, and evaluate their regulatory effects on folate metabolism and gut microbiota in folate-deficient mice. MethodsHigh-throughput cultivation and screening were performed to isolate folate-producing probiotics. Whole-genome sequencing, pathway reconstruction, and metabolite profiling in fermented milk were used to explore folate biosynthesis pathways and potential microbial cross-feeding interactions. A folate-deficient mouse model was established to evaluate the effects of a probiotic cocktail on serum folate, homocysteine (Hcy) levels, and gut microbiota composition using microbiological assays, biochemical analyses, qPCR, 16S rRNA gene sequencing, alpha diversity analysis, principal coordinates analysis (PCoA), and Linear discriminant analysis Effect Size (LEfSe) analysis. ResultsOver 1,000 bacterial isolates were obtained, and over 10 strains, mainly belonging to Lactobacillus, Bifidobacterium, and Bacillus, showed folate production levels above 100 ng/mL. Genomic analysis revealed that most selected probiotic strains lacked genes involved in para-aminobenzoic acid (pABA) biosynthesis but retained downstream folate synthesis modules, suggesting a potential dependence on pABA-producing gut commensals for precursor supply through microbial cross-feeding. In fermented milk, probiotic strains mainly produced bioactive folates (5-MeTHF and THF), with strain-specific production capacities; L. plantarum, W. coagulans, and B. animalis subsp. lactis significantly increased 5-MeTHF levels in fermented milk. In vivo, high-dose probiotic intervention significantly elevated serum folate (p<0.01) and reduced Hcy (p<0.05) in folate-deficient mice, while medium-dose intervention showed no significant effects. The probiotic strains colonized the mouse gut in a dose-dependent manner: high-dose group exhibited >4,000-fold increase in relative abundance (Bifidobacteriaceae and Bacillaceae enriched), medium-dose group only enriched Bacillaceae, and low-dose group showed no effective colonization. High dose probiotic treatment enhanced gut microbial species diversity (increased Shannon index) and restored folate deficiency-induced gut microbiota dysbiosis (PCoA clustering closer to normal group). ConclusionThis study screened high folate-producing probiotic strains and demonstrated their ability to synthesize active 5-MeTHF, which may rely on microbial cross-feeding in gut microbiota. Furthermore, we demonstrated that folate-producing probiotic intervention significantly improves folate status and Hcy metabolism and restores gut microbiota homeostasis in folate-deficient mice. These findings suggensted that such probiotics could serve as a safer, more physiological intervention for folate deficiency and hyperhomocysteinemia, especially in populations with MTHFR polymorphisms.

microbiology↗

bioRxiv2026

Mouse models with human antibody repertoires for inducing multiple lineages of HIV-1 broadly neutralizing antibodies

The complementarity determining region (CDR) 1, 2 and 3 of antibodies are the principal antigen contact sites. The heavy chain CDR3 (CDR H3) is highly variable, because it includes random nucleotide additions by the terminal deoxynucleotidyl transferase (TdT). Some broadly neutralizing antibodies (bnAbs) against the human immunodeficiency virus-1 (HIV-1) rely heavily on CDR H3 to recognize conserved epitopes on HIV-1 Envelope (Env) protein. Elicitation of comparable bnAbs is a prime goal of HIV-1 vaccine development, but the shortage of precursor antibodies with suitable CDR H3s in human repertoire is a major challenge for immunogen design. To aid this effort, we generated six mouse models for inducing bnAbs against major HIV-1 Env epitopes. In each mouse model, the immunoglobulin heavy and light chain loci were engineered to predominantly rearrange the germline V, D and J segments of a bnAb lineage. Owing to CDR3 diversity, only a small subset of the V(D)J recombination products may encode variable regions that can engage bnAb epitopes with sufficient affinity to initiate immune response. Therefore, these mouse models can be used to test and optimize immunization strategies to induce bnAbs from rare and diverse precursors in complex antibody repertoires.

immunology↗

bioRxiv2026

Maturation of HIV-1 neutralizing antibodies in a germinal center conditional expression mouse model

In germinal centers, activated B cells modify their antigen receptors through somatic hypermutation (SHM), followed by antigenic selection that favors expansion of high affinity B cells. The affinity maturation process is critical for development of broadly neutralizing antibodies (bnAbs) against the human immunodeficiency virus-1 (HIV-1). BnAbs have been isolated from some people living with HIV-1. Because these antibodies target conserved epitopes of the HIV-1 Envelope (Env) protein, they inhibit a broad spectrum of viruses. Eliciting bnAbs by vaccination is a top priority for HIV-1 prevention, but reproducing the lengthy maturation of bnAbs is a major challenge. The problem is typified by VRC01 class antibodies, which recognize the CD4 binding site of HIV-1 Env protein. To reach the CD4 binding site, antibodies need to navigate through adjacent glycans. Accommodating the glycans requires multiple SHMs in germinal center (GC) B cells, including infrequent events. For this reason, VRC01 vaccine development often stalls at this point. We have generated a mouse model aimed at providing a potential solution for navigating this vaccine design impediment. To this end, we made a mouse model that expresses a stalled VRC01 intermediate conditionally in GC B cells. This system has three advantages: 1) direct expression of the intermediate obviates prior immunization steps, thereby shortening the immunization scheme; 2) the conditional expression system bypasses tolerance control checkpoints that sometimes delete B cells expressing bnAbs; 3) the intermediate responds to immunization in GCs, the physiological site of affinity maturation. With this model, we established an immunization method to mature the VRC01 intermediate into heterologous neutralizing antibodies against viruses with a native glycan shield. Since high mutation load is common among bnAbs, the germinal center conditional expression system could provide a general tool for boost immunogen design to overcome roadblocks in the maturation pathway. Author summaryIn response to antigenic stimulation, cognate B cells become activated and form germinal centers in lymphoid tissues. Germinal center B cells modify their antigen receptors through somatic hypermutation (SHM) of immunoglobulin variable region gene exons, with antigen selecting for high affinity B cells by providing survival advantage. This mechanism accounts for antibody affinity maturaton over the gradual course of an immune response. Affinity maturation is critical for generating potent, neutralizing antibodies against diverse strains of the human immunodeficiency virus-1 (HIV-1). These broadly neutralizing antibodies (bnAbs) are heavily mutated, reflecting lengthy affinity maturation over years of chronic infection. Recapitulating the affinity maturation process is a major challenge for bnAb induction by vaccination. In immunization experiments, bnAb development often stalls at rate limiting steps that involve infrequent, but functionally important, mutational events. Overcoming such obstacles requires boost immunogens that can stimulate the stalled B cells to acquire the requisite mutations. To this end, we recapitulated the maturation arrest of a bnAb lineage by expressing a stalled antibody in mouse germinal center B cells. Using this mouse model, we developed boost immunization conditions that advanced the antibody maturation beyond a roadblock to attain neutralizing activities against heterogenous viruses.

immunology↗

bioRxiv2026

The enhanced multi-tissue atlas of regulatory effects in cattle

Cattle are integral to global food security, yet the molecular architecture of their complex traits remains poorly understood. Here, we present the Cattle Genotype-Tissue Expression (CattleGTEx) Phase 1 resource (https://cattlegtex.farmgtex.org/), a substantial expansion of the pilot study. By leveraging 12,422 RNA-seq profiles across 43 tissues and 82 breeds, we characterized 433,972 primary and 161,428 non-primary regulatory effects spanning seven molecular phenotypes. This high-resolution atlas resolves 75% of GWAS signals for 44 complex traits, significantly addressing the "missing regulation" in livestock. We propose a genetic regulatory model demonstrating how variants across multiple biological layers interact with specific biological contexts to shape phenotypic variation. Furthermore, CattleGTEx elucidates mechanisms underlying adaptive evolution between Bos taurus and Bos indicus, as well as artificial selection in dairy and beef breeds. Finally, by mapping evolutionary constraints on these regulatory effects, we demonstrate the translational value of this resource for prioritizing causal variants in human complex diseases. Together, Phase 1 of CattleGTEx provides a transformative framework for functional genomics, precision breeding, and comparative genetics.

genetics↗

bioRxiv2026

AI-driven discovery and engineering of human endogenous nanocage proteins for mRNA delivery

Safe and effective gene delivery remains a central challenge for therapeutic applications. While non-viral and viral vectors have enabled substantial progress, their reliance on non-human components often triggers immune responses, limiting their use in chronic treatments. Here, we developed DeepDelivery, an artificial intelligence-driven platform to repurpose human proteins for mRNA delivery. An unbiased screening of the human proteome nominated 512 candidates, with experimental validation confirming that 80% of top-ranked hits form mRNA-encapsulating particles and mediate efficient functional delivery in human cells without provoking detectable inflammation. Notably, multiple tripartite motif (TRIM) family proteins, typically linked to antiviral responses, exhibited strong assembly and delivery activity. Quantitative analysis and interpretation of the model revealed structural domains that govern nanocage formation, enabling domain-guided engineering of TRIM25 variants with enhanced function. Our work establishes a generalizable framework for discovering human-derived delivery vehicles and provides a path toward programmable, non-immunogenic mRNA therapeutics.

synthetic biology↗

bioRxiv2026

Systemic and Local Delivery of siRNA to the CNS and Periphery via Anti-IGF1R Antibody Conjugation

siRNA delivery platforms capable of accessing both central and peripheral tissues are critically needed to expand the therapeutic potential of oligonucleotides. To address this, we developed a novel siRNA-antibody conjugate by attaching an Hprt-targeting siRNA to an engineered antibody shuttle. This shuttle targets the insulin-like growth factor 1 receptor (IGF1R) using a fused antibody fragment (Clone F) and utilizes an antibody backbone with no tissue-relevant binding in this study. The resulting conjugate, designated Clone F-Hprt, demonstrated robust in vivo knockdown across multiple tissues. Clone F-Hprt demonstrated enhanced penetration into central nervous system (CNS) tissues compared to unconjugated siRNA following intracerebroventricular (ICV) and intravenous (IV) administration. In peripheral tissues, Clone F-Hprt achieved widespread knockdown in muscle, heart, and lung, consistent with IGF1R expression. The conjugate was well tolerated across all routes, including with repeated dosing. Although several receptor-mediated approaches for CNS delivery are progressing to the clinic (e.g., targeting the transferrin receptor), clinical validation remains to be demonstrated. Our findings highlight IGF1R as an alternative receptor capable of supporting delivery across both central and peripheral tissues, offering a complementary strategy for expanding the therapeutic landscape of oligonucleotide delivery.

neuroscience↗

bioRxiv2026

Engineering Functionality-Optimized Fully Human B7-H3 CAR T Cells for Enhanced Solid Tumor Therapy

B7-H3 is a cell surface protein overexpressed in many solid tumors and an attractive target for chimeric antigen receptor (CAR) T cell therapy. The most clinically advanced B7-H3 CARs are derived from murine monoclonal antibodies (mAbs) 376.96 and MGA271, which are now in phase 1/11 trials. However, non-human mAb sequences can provoke immune responses, leading to CAR T-cell rejection and therapeutic failure. Although scFv humanization reduces this risk, residual foreign residues within the variable domains remain. To overcome this limitation, we used in vitro phage display to generate fully human B7-H3-specific scFvs for CAR design. In pancreatic cancer, neuroblastoma, and glioblastoma xenograft models, CAR T cells incorporating the lead human binder Y111 were well tolerated and demonstrated superior antitumor activity compared with 376.96- and MGA271-based CARs. Y111 CAR treatment induced complete responses, tumor rejection, and significant survival benefits, identifying Y111 as a promising fully human B7-H3 CAR for solid tumors.

immunology↗

bioRxiv2025

Engineered translation release factor 1 suppresses disease-causing nonsense mutations and enables multi-site nonstandard amino acids incorporation

Nonsense mutations convert sense codons into premature termination codons (PTC), resulting in early termination of translation of mRNAs, underlie [~]11% of human genetic diseases. Restoring translation of genes carrying nonsense mutations remains a major therapeutic challenge. Here we present OPENER (Overexpression of Protein-engineered eRF1 for Nonsense Elision and Readthrough), a strategy to efficiently suppress nonsense mutations based on engineered variants of the eukaryotic translation termination factor eRF1. Through saturation mutagenesis of the human eRF1 N-domain, we identified variants, notably eRF1S77E, that promote efficient readthrough of all three PTCs (UAG, UGA, UAA) and rescue 12 pathogenic PTCs reporters in multiple disease contexts. Systemic delivery of OPENER-S77E via AAV8 in a Duchenne muscular dystrophy mouse model (DmdQ995X) restored dystrophin expression, improved muscle function, and ameliorated pathology without detected toxicity. Furthermore, when combined with orthogonal engineered aminoacyl-tRNA synthetase/tRNA pairs, OPENER-S77E enabled efficient, multi-site incorporation of nonstandard amino acids (BocK and AzF) into a single protein in mammalian cells, achieving efficiency of 27.77% and 19.83%, respectively. The incorporation efficiency of BocK was further enhanced to 32.80% in conditional eRF1-knockout cells. OPENER thus provides a platform for treating nonsense-mediated diseases and expands the synthetic biology toolkit for precise protein engineering.

synthetic biology↗

bioRxiv2025

Yuanyang allele pairs enable engineered obligate co-inheritance for population replacement and suppression

Mendels law of segregation, which dictates independent assortment of alleles, is a cornerstone of genetics. Here, we present the Yuanyang allele pair (YYAP), an engineered underdominance gene drive system that enforces obligate co-dependency between homologous alleles via synthetic toxin-antitoxin circuits. This design produces a striking deviation from classical Mendelian segregation: YYAP alleles cannot segregate independently, reshaping inheritance outcomes without altering the physical mechanics of meiosis. In Drosophila melanogaster, optimized YYAP strain K711 exhibits >99% hemizygous lethality when crossed with wild type, while maintaining stable transmission and high fitness in transheterozygotes. Cage experiments demonstrate efficient population replacement, positioning YYAP as a confined, resistance-proof alternative to CRISPR homing gene drives. Release of only males represents a self-limiting suppression strategy that was also successful in cage experiments. By imposing a near-complete postzygotic incompatibility, YYAP establishes a programmable framework that not only supports pest management, but also enables modeling of reproductive isolation and allelic co-dependency, thereby creating opportunities to explore speciation and broader synthetic inheritance systems in ecology and evolution.

molecular biology↗

bioRxiv2025

A multi-tissue atlas of genetic regulatory effects in sheep

Characterizing the impact of genomic variants on genome function and ultimately complex traits in livestock is essential for the development of sustainable precision agriculture and comparative genomics. Here, as part of the Farm animal Genotype-Tissue Expression (FarmGTEx) project, we present the pilot phase of the SheepGTEx resource through analyzing 6,761 RNA-sequencing samples of 51 primary tissues in a multi-breed population of sheep. We identify millions of regulatory variants associated with seven types of molecular phenotypes, and fine-map 322,468 primary and 114,017 non-primary effects, revealing a high degree of regulatory allelic heterogeneity. We systematically characterize the pleiotropic effects of these variants on molecular phenotypes, assess their context-specific regulatory patterns across tissues, breeds, sexes, and developmental stages, as well as explore their evolutionary constraints across mammals. Finally, we demonstrate the substantial potential of the SheepGTEx resource (https://sheepgtex.farmgtex.org), by providing examples of regulatory mechanisms underpinning 34 complex traits, population divergence between European and Asian breeds, and adaptive evolution in sheep over the past ten millennia.

genomics↗

bioRxiv2025

Transposon targeting non-coding RNA transcription targets G/C-rich tracts and is facilitated by an intrinsically disordered protein in Tetrahymena

Tetrahymena is a well-established ciliate model organism, known for its nuclear dualism and unique mechanism for transposon defense, wherein transposons are kept within the highly heterochromatinized micronucleus (MIC), which is transcriptionally inert except during meiosis. The discovery of preferential transcription in the meiotic MIC at regions enriched with transposons, and the identification of MIC transcription regulatory proteins, emphasizes the necessity to elucidate the underlying mechanisms driving this process. In this study, we demonstrate that G/C-rich tracts are overrepresented in meiotic non-coding RNA (ncRNA) transcription regions and that RNA polymerase II (Pol II) is highly enriched at and around these tracts. Further analysis revealed that Pol IIs association with G/C-rich tracts is not abolished in cells lacking Rib1, a Mediator complex-associated protein essential for MIC ncRNA biogenesis. Nevertheless, in the absence of Rib1, Pol II showed abnormal association with the meiotic MIC chromatin, suggesting that Rib1 is critical for maintaining Pol IIs binding specificity. Through Rib1 truncation analysis, we found that the intrinsically disordered region, which contains putative phase-separating peptides, is crucial for its function. Disruption of phase-separation, either by deleting these peptides or by treating cells with a phase-separation disruption reagent, leads to aberrant localization of both Rib1 and Pol II on the MIC chromatin, implicating that Rib1 likely facilitates the MIC ncRNA transcription via phase-separation.

molecular biology↗

bioRxiv2025

Population density triggers wing dimorphism via NlNompC-mediated insulin signaling in Nilaparvata lugens

The Nilaparvata lugens employs wing dimorphism as a key adaptive strategy to environmental heterogeneity. While hormonal pathways and transcription factors governing nutrient-induced wing plasticity are known, how population density triggers developmental divergence remains unresolved. Here, we mechanistically dissect density-dependent wing morph determination, revealing tactile inter-individual contact as the primary signal. High-density conditions amplify gentle-touch frequency, which is detected by mechanosensitive ion channels NlNompC and NlNMDARs. Genetic silencing or pharmacological inhibition of these channels abolished density-induced long-winged morphogenesis. The conserved role of NlNompC in gentle-touch sensation was validated by rescuing tactile perception deficits in Drosophila nompC mutants. Crucially, NlNompC integrates tactile cues into insulin/insulin-like growth factor signaling (IIS): crowding-driven mechanical stimuli upregulate NlIlp3, while suppressing NlInR2, to activate wing elongation programs. Epistasis experiments confirmed IIS as the key downstream pathway, with co-silencing NlInR2 or NlFoxO rescuing the short-winged phenotype induced by NlNompC knockdown or low population density, silencing NlIlp3 or NlInR1 rescuing the long-winged phenotype induced by high population density. Our work uncovers a mechano-endocrine axis linking tactile perception to developmental plasticity, bridging ecological cues with molecular pathways. These findings redefine density sensing beyond chemical modalities and offer actionable targets for disrupting pest dispersal strategies, advancing sustainable agriculture.

molecular biology↗

bioRxiv2025

PATTY corrects open chromatin bias for improved bulk and single-cell CUT&Tag profiling

Precise profiling of epigenomes is essential for better understanding chromatin biology and gene regulation. Cleavage Under Targets & Tagmentation (CUT&Tag) is an efficient epigenomic profiling technique that can be performed on a low number of cells and at the single-cell level. With its growing adoption, CUT&Tag datasets spanning diverse biological systems are rapidly accumulating in the field. CUT&Tag assays use the hyperactive transposase Tn5 for DNA tagmentation. Tn5s preference toward accessible chromatin alters CUT&Tag sequence read distributions in the genome and introduces open-chromatin bias that can confound downstream analysis, an issue more substantial in sparse single-cell data. We show that open-chromatin bias extensively exists in published CUT&Tag datasets, including those generated with recently optimized high-salt protocols. To address this challenge, we present PATTY (Propensity Analyzer for Tn5 Transposase Yielded bias), a comprehensive computational method that corrects open-chromatin bias in CUT&Tag data by leveraging accompanying ATAC-seq. By integrating transcriptomic and epigenomic data using machine learning and integrative modeling, we demonstrate that PATTY enables accurate and robust detection of occupancy sites for both active and repressive histone modifications, including H3K27ac, H3K27me3, and H3K9me3, with experimental validation. We further develop a single-cell CUT&Tag analysis framework built on PATTY and show improved cell clustering when using bias-corrected single-cell CUT&Tag data compared to using uncorrected data. Beyond CUT&Tag, PATTY sets a foundation for further development of bias correction methods for improving data analysis for all Tn5-based high-throughput assays.

bioinformatics↗

bioRxiv2025

Tau deletion results in sex-dependent modulation of synaptic weakening in rat hippocampus

Tangles, a defining characteristic of Alzheimers disease (AD), are composed principally of hyperphosphorylated and misfolded tau species. However, dysregulation of tau precedes tangle formation by many years and is associated with cognitive decline, the best functional correlate of which is synaptic weakening and eventual synaptic loss. Although tau is present at synapses, its normal synaptic function is poorly understood - information vital to the rational development of tau-modifying therapies. Since rats have a greater cognitive repertoire than mice and display more robust signs of tau pathology in AD models, we developed a tau knockout (Mapt-/-) rat to investigate the impact of tau elimination on synaptic function. We observed that long-term depression (LTD), a form of synaptic weakening, is enhanced in the hippocampus of male, but not female, rats. This enhanced LTD was dependent on the synaptic activation of group I metabotropic glutamate receptors and involved altered synaptic actin polymerization. These studies therefore provide mechanistic insights into how tau modulates synaptic function via regulation of the actin cytoskeleton. Our findings are relevant to the understanding of the physiological roles of synaptic tau, the functional consequences of tau-lowering therapies, and the influence of sex in AD susceptibility.

neuroscience↗