Biology subjects

Chen, Y.

Publications and source records attributed to Chen, Y..

At least 55 records · Page 3Linked to original sources

bioRxiv2026

Prime editing enables high-throughput identification and characterization of selective MutSβ inhibitors

DNA mismatch repair (MMR) maintains genome stability but paradoxically drives expansion of pathogenic repeats responsible for trinucleotide repeat disorders. Attenuating repeat instability through targeted inhibition of MMR is therefore a therapeutic strategy of interest; however, progress is constrained by a lack of robust methods for defining and isolating MMR subpathways. We exploited features of prime editing to profile the effects of core MMR genes on thousands of programmed DNA mispairs in cells and resolved distinct MMR processes, including a noncanonical, loop-directed mechanism. Guided by these results, we built a set of scalable reporters that detect loss of separable MMR processes and screened ~72,000 small molecules for activity against MutS{beta}-directed MMR. This effort identified a novel series of MutS{beta} inhibitors that reduced (CAG)n expansion in a cell model. Altogether, this study establishes several methods for systematically interrogating MMR, with demonstrated capacity to identify inhibitors of therapeutic value.

bioengineering↗

bioRxiv2026

Multiscale Network Disruption of Auditory-Language Circuits Underlying Auditory Hallucinations in Schizophrenia

Background: Auditory verbal hallucinations (AVH) are among the most disabling symptoms of schizophrenia, yet the network-level mechanisms linking auditory dysfunction to hallucination severity remain poorly characterized, limiting targeted therapeutic development. Methods: Using resting-state fMRI and high-resolution surface-based parcellation (HCP-MMP), we examined auditory-language functional connectivity and mesoscale network organization in 56 patients with schizophrenia and 22 healthy controls (primary dataset, N=78). Pairwise auditory-language connectivity associations with hallucination severity (PANSS P3) were examined alongside auditory network community structure, assortativity, hub organization, and routing efficiency. To further characterize these parcel-level findings at the vertex level, we applied a region-growing approach to identify auditory-frontal connectivity patterns maximally associated with severity. In silico perturbation analyses tested the causal role of belt cortex connectivity. Key findings were independently replicated in 93 patients from the Human Connectome Project for Early Psychosis (HCP-EP), for a combined total of 171 participants. Results: Auditory-language connectivity disruptions were concentrated in belt cortex and specifically implicated ventral what-stream connections, with a vertex-wise analysis converging on the same anatomy. Auditory network segregation scaled with hallucination severity, with belt cortex emerging as the primary integrative hub governing auditory-to-language routing efficiency. Perturbation analyses showed that strengthening earlier hierarchy auditory regions reduced network segregation more than strengthening later-hierarchy regions. Reduced belt cortex coupling and elevated network segregation replicated independently in the HCP-EP sample. Conclusions: Auditory network disorganization scales with hallucination severity and replicates across independent samples, with belt cortex as the critical locus of connectivity disruption and network integration failure, identifying it as a candidate neuromodulatory target.

neuroscience↗

bioRxiv2026

Bottom-up engineering of EV-mimetic vesicles reveals selective protein loading and modulates cellular uptake and biodistribution

Biological systems such as extracellular vesicles (EVs) are highly sophisticated and functionally diverse. Despite growing recognition of EVs' roles in health and disease through mediating intercellular communication, their inherent heterogeneity and challenges in purity and yield hinder their mechanistic research and clinical translation. To address this gap, we sought to translate essential EV properties into a controllable and simplified platform by engineering biomimetic synthetic vesicles (SVs) incorporating defined proteins and lipids. Using microfluidics, we generated SVs loaded with bulk membrane and cytosolic proteins from cancer cells, as well as individual organotropism-associated integrins. Bulk membrane protein incorporation into SVs reduced surface charge, modified lipid profiles, and enhanced cellular uptake, while integrin incorporation altered biodistribution. To investigate protein loading, we profiled input materials and SVs by mass spectrometry, identifying features linked to high incorporation, such as low molecular weight, positive charge, high isoelectric point, and predicted stability, globularity, lipidation, and amphipathic helices. This work presents a synthetic platform for dissecting the roles of EV-associated features and cargo, while providing insights into protein properties relevant to the optimization of delivery systems.

bioengineering↗

bioRxiv2026

Simultaneous multi-area recordings in macaque frontoparietal cortex during a manual object-interaction task

Dexterous hand control is essential for daily activities and a top restoration priority for people with tetraplegia, yet neurophysiological datasets suitable for studying and decoding naturalistic hand behavior remain scarce. Most available recordings constrain movements to a small number of degrees of freedom or cover only a single stereotypical grasp-and-hold structure. Moreover, previous brain-computer interface (BCI) studies have largely relied on signals from a single cortical area, even though dexterous hand control is distributed across an interconnected frontoparietal network. To address these limitations, we designed a paradigm that elicits rich hand movements across 40 distinct hand-object interaction conditions. We recorded simultaneous frontoparietal activity with hand kinematics from a rhesus macaque performing them. Neural activity was recorded from the primary motor cortex, anterior intraparietal area, and ventral premotor cortex using microelectrode arrays spanning 1,920 channels, while a multi-camera markerless motion-capture system acquired video from which kinematics were extracted offline. The dataset comprises data from 20 sessions, including processed neural features, synchronized 3D coordinates of hand and elbow keypoints, and trial-level metadata including task conditions and event timing. We further provide technical validation, including a neural decoding benchmark with multiple algorithms for continuous keypoint coordination reconstruction. We found that cross-day and cross-task decoding performance varied among algorithms. Variation in channel availability leads to different performance degradation curves in different algorithms. This task-rich dataset offers a valuable resource for investigating the neural mechanisms of dexterous hand control and for advancing the performance of motor BCIs.

neuroscience↗

bioRxiv2026

Evolutionary signatures of self-incompatibility genes in grasses: high diversity, trans-generic polymorphism and co-evolution

In many flowering plants, self-incompatibility (SI) is a genetically controlled recognition system that prevents self-fertilization, thereby promoting outcrossing and maintaining genetic diversity within populations. The gametophytic SI system in grasses (Poaceae) is governed by two multiallelic loci, S and Z, each locus comprising of three genes governing the initial recognition between pollen and stigma. Identifying these genes establishes the molecular basis of SI in grasses, but how its unique two-locus architecture has shaped the evolution of the underlying loci and recognition genes remains largely unexplored. Here, we report targeted sequence capture of SI genes in 362 genotypes across nine forage grass species, revealing extensive allelic richness and sequence diversity. The SI genes exhibited elevated nucleotide diversity ({pi}) (0.134 < {pi} < 0.403) and great amino acid sequence divergence, ranging between 48.2-58.0% for the female determinants (sS and sZ) and 66.5-83.4% for the male determinants (SI-DUF247). The SI-DUF247 proteins also displayed trans-generic polymorphism, indicating that alleles predate speciation. Phylogenetic analysis of SI determinants showed congruence at both S- and Z-locus, consistent with co-evolution of recognition partners. Our results demonstrate that the unique two-locus SI system in grasses shares evolutionary characteristics with other SI systems, suggesting that their reproductive function is shaping their evolution. These findings also indicate that the grass SI loci are under long-term balancing selection to maintain recognition specificity while creating sufficient allelic diversity. Our study provides comprehensive sequence resources for SI genes and new insights into the evolution of the unique two-locus SI system of grasses.

plant biology↗

bioRxiv2026

A Novel NO Donor 3A72 Activates Mitochondrial-Associated Endoplasmic Reticulum Membrane Structures to Induce Ferroptosis in Triple-Negative Breast Cancer

Triple-negative breast cancer (TNBC) remains a major clinical challenge due to a lack of effective interventions and severe drug resistance. Disrupting tumor metabolism using nitric oxide (NO) donors to drive ferroptosis represents a promising therapeutic strategy. Here, we developed 3A72, a novel furan-coumarin-based NO donor with potent anti-TNBC efficacy. In vitro and in vivo studies demonstrated that 3A72 significantly suppresses TNBC cell proliferation and restricts xenograft tumor growth. Notably, its efficacy matches the first-line drug paclitaxel but with enhanced safety and reduced systemic toxicity. Mechanistically, 3A72 induces ferroptosis in triple negative breast cancer (TNBC) cells via a synergistic dual-pathway mechanism. Initially, 3A72 releases intracellular NO to trigger cytoplasmic calcium overload, followed by high-affinity binding to both inositol 1,4,5-trisphosphate receptor (IPR) and acyl-CoA synthetase long-chain family member 4 (ACSL4). Binding to IP3R provokes mitochondrial calcium overload and a massive burst of reactive oxygen species (ROS), while concurrent ACSL4 activation drives essential membrane phospholipid remodeling. Crucially, our transcriptomic and structural predictions reveal that while ACSL4 exhibits a broader distribution across organelle membranes, its functional association with IP3R spatially converges at the endoplasmic reticulum membranes associated with mitochondria (MAMs). This subcellular niche closely couples IPR-mediated ROS generation with ACSL4-driven lipid remodeling, accelerating lethal malondialdehyde (MDA) accumulation and triggering irreversible ferroptosis. Overall, these findings highlight the MAMs calcium-lipid metabolic hub as a promising structural scaffold for antitumor drug development.

cancer biology↗

bioRxiv2026

A kinetic-aware approach to infer metabolic variations and flux using transcriptomics and metabolomics data

Assessing metabolic variations and flux quantities enable systematic understandings of metabolic shifts, reprogramming, adaptation and interactions in human diseases. However, omics-based estimation of metabolic flux and its variation remains challenging due to several fundamental limitations: the need for disease and tissue context specific metabolic model; nonlinear enzyme kinetic model that links enzyme and substrate changes to reaction flux; partial, unpaired, and snap-shot measurements across omics modalities; and uncertainty in computational prediction. Here, we present Michaelis-Menten model-based Flux Estimation Analysis (mmFEA), a Monte Carlo framework for estimating condition-specific flux changes by integrating paired or unpaired metabolomics and transcriptomics (or proteomics) data. mmFEA separates each reaction-rate change into enzyme- and substrate-associated components and assess reaction rate using Michaelis-Menten kinetics equation. A baseline metabolite saturation rate is introduced by integrating protein language model predicted kinetic parameters and human baseline level metabolic concentration to enable kinetic-aware integration of unpaired substrate and enzyme level measurements. Distribution of metabolic flux and variations between conditions are further computed using MCMC sampling by treating Michaelis-Menten-derived marginal flux distribution as prior and coherency in flux balance as likelihood. To benchmark mmFEA, we generated an in-house multi-omics data set including transcriptomics, metabolomics, metabolic activity functional assay, and CRISPR screening data using pancreatic cancer cell line system treated by APEX1 inhibitors. We demonstrated that mmFEA could accurately capture experimentally observed metabolic changes and achieved a better performance than all baseline methods. Our analysis revealed the necessity in using both substrate and enzyme modality and kinetic aware model in metabolic flux assessment. Further analysis using independent pancreatic cancer cohorts further validated the robustness of mmFEA, supporting integration of condition-linked unpaired data. Pan-cancer and spatial multi-omic applications demonstrated the use of mmFEA for resolving context-dependent metabolic variation when direct flux measurements are unavailable. Together, mmFEA provides a mechanistically grounded framework for estimating relative metabolic flux changes and their uncertainty from heterogeneous omics data.

systems biology↗

bioRxiv2026

The uplift of the Qinghai-Tibetan Plateau reshaped genome architecture and diversification of Asian torrent catfishes

Tectonic uplift and mountain building are major drivers of species diversification and adaptation, yet how they reshape genome architecture and promote evolutionary innovation remains poorly understood. Here, we generated multiple chromosome-level genomes for Asian torrent catfishes (Sisoridae) and performed phylogenomic and comparative genomic analyses. Our results support an Asian origin of Sisoridae and provide a refined phylogenetic topology for catfishes. Comparative analyses revealed extensive chromosomal rearrangements during sisorid evolution, indicating highly dynamic genome architectures. The timing of sisorid diversification overlaps with major phases of regional tectonic change, and analyses of phylogenetic discordance indicate heterogeneous contributions from incomplete lineage sorting and introgression. Elevational distribution was associated with variation in estimated molecular evolutionary rates, while exploratory scans identified lineage-specific candidates for selection and convergent evolution. Candidate coding and non-coding changes occur near genes with known roles in fin development, body patterning, and liver biology, but their effects on sisorid traits remain to be tested. Together, our results demonstrate how tectonic uplift reshaped genome architecture and diversification in Asian torrent catfishes and provide new insights into the genomic basis of adaptation in mountainous freshwater ecosystems.

evolutionary biology↗

bioRxiv2026

A PVH-to-parabrachial BDNF circuit mediates non-aversive feeding suppression

Parabrachial nucleus (PBN) CGRP neurons mediate aversive feeding suppression, but PBN circuitry governing homeostatic, non-aversive feeding suppression remains poorly understood. Here, we identify a circuit in which paraventricular hypothalamus (PVH) neurons innervate BDNF-expressing ventrolateral/dorsolateral PBN (vl/dlPBNBDNF) neurons, which project to multiple hypothalamic nuclei. Refeeding strengthens excitatory and weakens inhibitory synaptic transmission in LPBN-projecting PVH neurons and preferentially induced Bdnf and Fos in vl/dlPBNBDNF neurons compared with elPBNCGRP neurons, whereas noxious LPS preferentially activated elPBNCGRP neurons. Gain- and loss-of-function experiments demonstrated that vl/dlPBNBDNF neurons are sufficient and necessary for feeding suppression without inducing conditioned taste aversion and that this effect require BDNF-TrkB signaling. In addition to hypothalamic inputs, vl/dlPBNBDNF neurons receive dense inputs from major downstream targets of elPBNCGRP neurons. Thus, vl/dlPBNBDNF neurons define a non-aversive feeding-suppression circuit positioned to integrate hypothalamic homeostatic signals with aversive signals, thereby coordinating food intake with internal energy needs and potentially harmful physiological conditions.

neuroscience↗

bioRxiv2026

High-SNR Whole-Brain Mesoscale Diffusion MRI Using Rotating-View Acquisitions (ROVER-dMRI)

Purpose: We aim to acquire and reconstruct high signal-to-noise ratio (SNR), whole-brain, mesoscale (isotropic submillimeter) diffusion MRI (dMRI) in vivo in a clinically feasible scan time. Methods: We present ROVER-dMRI, a unified rotating-view acquisition and super-resolution reconstruction framework. Thick slices (up to 10 mm)acquired across many rotated orientations improve the base SNR, and a shared multi-resolution hash-encoded implicit neural representation (INR) with per-direction MLP head and a physics-informed, Bloch-simulated slice-profile forward model reconstructs these views into a continuous isotropic volume (up to 13x super-resolution) in a self-supervised manner. ROVER-dMRI was evaluated in vivo on human brain (0.78 mm isotropic and 0.5 mm isotropic) and monkey brain (0.6 mm isotropic) across MRI platforms with varying gradient performance, and benchmarked against gSlider-SMS and least-squares super-resolution reconstruction (LS-SRR). Results: At 0.78 mm isotropic resolution, ROVER-dMRI diffusion- weighted images achieved higher SNR than the vendor product sequence, whose images were limited by the noise floor, while its directionally encoded color (DEC) maps showed lower noise than gSlider. When reducing the number of views from 20 to 13 (reducing the scan time by 65% ), ROVER-dMRI acquisition/reconstruction preserved all fine details in the fiber orientations. In the monkey brain, its DEC map matched a 60-direction gSlider acquisition at only 40% of the scan time. ROVER-dMRI preserved coherent fiber-orientation-distribution (FOD) structure, including crossing fibers, and recovered fine details in the cerebellum at 0.5 mm isotropic, that are not visible at 0.78 mm resolution. Compared to state-of- the-art 0.5 mm methods, ROVER-dMRI reduced scan time by 73% while acquiring more diffusion directions. Conclusion: ROVER-dMRI offers a practical route to high-SNR whole-brain mesoscale diffusion imaging in vivo, with the pulse sequence and reconstruction pipeline released as open source. KEYWORDS: diffusion MRI, super-resolution, implicit neural representation, hash encoding, physics informed learning

neuroscience↗

bioRxiv2026

Octave: Scale-resolved Evaluation of Spatial Gene Expression Prediction from Histology

Spatial gene expression prediction from histology is typically evaluated by the mean per-gene Pearson correlation (PCC). PCC does not distinguish spatial scales: coarse tissue organization alone can earn most of the score. A domain oracle makes this precise: given an image-derived partition of the tissue, the predictor that assigns each domain its measured mean expression is the best that any predictor constant on that partition can do. On a widely used benchmark with a ~100 um pitch, a learnable version that estimates each domain mean from training data reaches 82% of the PCC of a trained model, and a partition of the spot coordinates alone, given measured means, reaches 123%. At that pitch the score rewards coarse spatial structure whatever its source. We introduce OCTAVE, a scale-resolved evaluation that filters prediction and measurement into spatial bands with widths in micrometers and scores their agreement in each band. On 16 um Xenium data, differences that look modest under PCC grow at finer scales: at ~20 um the oracle shortfall relative to the trained model is 2.4 times its PCC shortfall at the median and exceeds it in all 13 specimens. Across 57 image encoders the finest band reorders 261 of the 1596 encoder pairs relative to PCC. The benchmark own finest band is 50 um wide, coarser than the scale at which these differences appear, so no score on that pitch can directly validate finer structure. OCTAVE reports how well a model predicts spatial expression at each spatial scale.

bioinformatics↗

bioRxiv2026

TRIM21 licenses pancreatic acinar fate by modulating BiP phase state through VCP-dependent retrotranslocation

The endoplasmic reticulum (ER) chaperone BiP/GRP78 sits at the center of the proteostasis network, coordinating unfolded protein response (UPR) signaling and supporting oncogenic programs of plasticity, metastasis, immune evasion, and chemoresistance. While BiP undergoes liquid-liquid phase separation in vitro, whether mammalian cells dynamically tune this physicochemical behavior to prevent functional exhaustion or pathological condensation under sustained ER stress has remained unclear. Here, we identify the E3 ubiquitin ligase TRIM21 as a phase-state regulator that suppresses BiP's liquid-to-solid phase separation, clearing, and preventing insoluble aggregates-thereby controlling BiP's localization and availability to sustain the adaptive UPR under ER stress. We found that during ER stress, BiP is prone to liquid-to-solid phase separation, a transition that renders the chaperone dysfunctional. TRIM21 is recruited to BiP, where it directly polyubiquitinates BiP at specific K547/553/554/556 sites with K6-, K27-, K33-, and K63-linked chains; VCP recognizes these marks and extracts BiP from the ER lumen via ER-associated degradation (ERAD), coupling ubiquitin tagging to retrotranslocation. This preserves chaperone availability and sustains adaptive UPR-a homeostatic mechanism broadly relevant to UPR-driven diseases. In vivo, genetic ablation of Trim21 in KrasG12D/+; Pdx1Cre/+ mice triggers aberrant BiP solidification while curtailing acinar-to-ductal transdifferentiation and tumorigenesis; notably, TRIM21 co-localizes with BiP condensates in pre-malignant human pancreatic lesions, underscoring the clinical relevance of this regulatory axis. Our findings define the TRIM21-BiP axis as a phase-control system at the interface of proteostasis and stress adaptation, offering a new framework with translational potential.

cell biology↗

bioRxiv2026

Therapeutic Potential of iPSC-Derived TH+FOXA2+ Neuronal Extracellular Vesicles in Parkinson's Disease Revealed by Organoid and Rodent Models

Background: Parkinson's disease (PD) is characterized by the progressive loss of midbrain dopaminergic (DA) neurons and aberrant alpha-synuclein (alpha-syn) aggregation, yet disease-modifying therapies that simultaneously retard neurodegeneration and foster regeneration remain lacking. Methods: In this study, we isolated extracellular vesicles (TH and FOXA2 double-positive cell-derived EVs) from TH and FOXA2 double-positive differentiated neural cells, a distinct midbrain floor-plate-derived neural cell population that co-expresses the floor-plate transcription factor FOXA2 together with TH and should therefore not be equated with conventional mature midbrain dopaminergic neurons, and systematically evaluated their therapeutic potential across three complementary models: A53T transgenic mice, 6-OHDA-lesioned rats, and 6-OHDA-treated human midbrain organoids. Integrative transcriptomic and single-cell sequencing analyses, together with toxicological evaluations in rodents and non-human primates, were performed to investigate the underlying mechanisms and safety profile. These TH and FOXA2 double-positive cells were generated using a fully suspension-based, matrix-free, and chemically defined differentiation system devoid of N2/B27 supplements and fetal bovine serum (FBS). This approach offers a simple, controllable, low-cost, and scalable platform with high batch-to-batch consistency for EV manufacturing. Throughout this study, the term "TH and FOXA2 double-positive cells" refers to this distinct TH and FOXA2 double-positive cell population and should not be interpreted as conventional terminally differentiated dopaminergic neurons. Results: Intranasal administration of TH and FOXA2 double-positive cell-derived EVs in A53T mice and 6-OHDA-lesioned rats significantly ameliorated motor deficits, increased nigral tyrosine hydroxylase (TH)-positive neuron counts, reduced alpha-syn aggregation, and suppressed gliosis. In human midbrain organoids, TH and FOXA2 double-positive cell-derived EVs preserved DA neuronal morphology and reduced GFAP and alpha-syn expression. Notably, when EVs were administered simultaneously with 6-OHDA modeling rather than after modeling was completed, the protective effect was stronger. Multi-omics analysis revealed that TH and FOXA2 double-positive cell-derived EVs reversed pathological signatures of interferon-responsive microglia and oxidative stress-adapted astrocytes, while restoring WNT- and non-canonical WNT-mediated intercellular communications. Safety evaluations showed no discernible organ toxicity. Conclusions: TH and FOXA2 double-positive cell-derived EVs exert neuroprotective effects across multiple PD models by modulating specific glial subpopulations and reinstating development-associated signaling pathways. Together with a fully suspension-based, matrix-free, and N2/B27-free differentiation process that enables low-cost, scalable, and highly reproducible manufacturing, TH and FOXA2 double-positive cell-derived EVs represent a promising therapeutic candidate for Parkinson's disease.

neuroscience↗

bioRxiv2026

Combined Loss of VHL and TSC1 Drives Clear Cell Renal Cell Carcinoma with Metabolic and Redox Reprogramming that Creates an NRF2 Dependency

Cancer genomics studies have implicated combined loss of VHL and TSC1 as sufficient to initiate clear cell renal cell carcinoma (ccRCC) in humans. Here, we engineered a mouse model with kidney-specific deletion of Vhl and Tsc1. VhlF/FTsc1F/FKsp-Cre+ mice developed multifocal renal cell carcinomas starting at 7 weeks of age with 100% penetrance, and the resulting Vhl-/-Tsc1-/- tumors recapitulated the histopathology of human VHL-/-TSC1-/- ccRCC. Integrated transcriptomic and metabolomic analyses of 4-week-old preneoplastic renal cortices deficient for Vhl and Tsc1 demonstrated heightened HIF and mTORC1 signaling and unexpectedly revealed activation of an antioxidant response regulated by NRF2 (NFE2L2). Biochemical, cell biological, multi-omic, and xenograft studies identified an NRF2 dependency in human VHL-/-TSC1-/- ccRCC cells. Altogether, we report a mouse model that recapitulates human VHL-/-TSC1-/- ccRCC, delineate metabolic and redox reprogramming driven by unrestrained HIF and mTORC1 activation in the renal cortex, and identify NRF2 as a potential therapeutic vulnerability.

cancer biology↗

bioRxiv2026

Agentic transcranial functional ultrasound imaging: @fUS

Functional ultrasound (fUS) imaging provides deep, wide-field access to brain function, but instrument cost and complex acquisition and analysis workflows restrict its wider adoption. Here we introduce @fUS, an agentic transcranial imaging platform with an open architecture that integrates purpose-built hardware with executable experimental skills and persistent structured memory. The system combines 128-channel, 16-bit acquisition at 125 MHz with GPU-based processing and enables functional imaging through the intact scalp and skull of mice, with approximately 100-m spatial resolution and 10-Hz temporal sampling, providing a basis for longitudinal studies without cranial-window surgery. Its agent connects scientific objectives to experimental design, direct instrument control and data analysis, retaining context across interactions and supporting inspectable workflows through text and hands-free voice control. Neuroscience trainees with limited engineering experience independently configured the system within 30 min. Agent-assisted exploration of whisker-stimulation datasets revealed low-frequency vascular changes beyond conventional response mapping, supported by complementary two-photon measurements of single-vessel diameter. By combining transcranial imaging with accessible instrument control and analysis, @fUS provides a foundation for wider adoption and larger, more diverse neuroscience datasets. More broadly, it offers a framework for scientific instruments in which measurement, computation and experimental reasoning are developed as parts of the same system.

bioengineering↗

bioRxiv2026

Loss of DNA Demethylase Enhances Arsenic Resistance Via Reducing of PIN2 Antisense Long Noncoding RNA

DNA methylation dynamics regulate diverse plant stress responses, but the mechanisms governing arsenic (As) tolerance through epigenetic pathways remain largely unknown. Here we report that Arabidopsis mutants lacking the DNA demethylase, REPRESSOR OF SILENCING (ROS1), show substantially enhanced As resistance. Integrating transcriptome and methylome data, we found that PIN-FORMED 2 (PIN2), encoding an auxin efflux carrier that also transports As out of cells, represents a key ROS1 target. In ros1, we observed increased methylation in the last exon of PIN2, a region functioning as the promoter for an antisense long non-coding RNA (lncRNA). Hypermethylation of the promoter suppresses the antisense lncRNA, which follows reduction of sense PIN2 transcription. As a result, PIN2 expression increases in ros1 mutants during As exposure, enhancing As tolerance. Analysis of ros1 pin2 double mutants confirmed that PIN2 acts downstream of ROS1 in As tolerance. Our study demonstrates an epigenetic pathway in which ROS1 regulates As tolerance by controlling PIN2 expression through antisense lncRNA-mediated transcriptional interference, offering new epigenetic strategies using plants in heavy metal contaminated environments.

plant biology↗

bioRxiv2026

Deep ancestral structure, admixture and peripheral persistence shape diversity in the Papilio bianor species complex

Rapid diversification can generate regional biodiversity through ancestral polymorphism, admixture, and ecological differentiation, while leaving complex genomic signals. We analysed whole-genome variation in 325 butterflies, including 166 individuals of the Papilio bianor species complex and six outgroup species, to reconstruct lineage relationships and demographic history. Nuclear genomic analyses recovered three major clades corresponding to the recognized species and placed the island lineage as sister to continental P. bianor. Analyses of 18,635 autosomal window trees revealed extensive genealogical discordance, with incomplete lineage sorting predominating among continental lineages and the strongest introgression signals involving island related ancestry. Demographic modelling supported early island continental divergence followed by continental diversification and ancient admixture. The best fitting fastsimcoal2 model inferred an admixed origin of the Eastern China lineage, while BPP analyses supported ancient island-related introgression into the Eastern China ancestor, Western Himalaya and southwestern Thailand. Peripheral populations exhibited pronounced genetic differentiation and distinct demographic histories; Western Himalaya additionally showed mitochondrial affinity with Yaeyama despite its placement within the Himalayan nuclear lineage. Together, these findings suggest that introgression among deeply differentiated ancestral populations and incomplete lineage sorting during rapid divergence jointly shaped lineage diversity in the P. bianor complex. This study provides an empirical framework for investigating how lineage diversity emerges rapidly during the early stages of speciation, particularly in groups with deep ancestral population structure.

evolutionary biology↗

bioRxiv2026

MIRCID: Inferred Hub-miRNAs Drive Cross-Task Improvements in Drug Mechanistic Modeling

Drug mechanism-of-action (MoA) modeling commonly relies on perturbational transcriptomes, but matched microRNA (miRNA) measurements are often unavailable. Inferred regulatory features offer a scalable way to reuse these data. Here, we present MIRCID, a framework comparing gene expression with inferred transcription factor (TF) activity and miRNA expression across pathway classification and similarity-based MoA retrieval. HubmiRNet infers 414 pan-cancer hub miRNAs (HubmiRs) from 977 L1000 landmark genes, achieving a Pearson correlation coefficient of 87.72\%; its 1,298-output variant also outperformed SiCmiR on the full-miRNA task (71.21\% versus 67.30\%). In the evaluated comparisons, miRNA augmentation provided more consistent gains than TF activity. Generic embedding controls showed model-dependent utility, while complementarity analyses identified a distinct, partially linearly recoverable representation that retained gene-derived structure. Illustrative rescue cases linked improved classification to biologically plausible miRNA patterns in samples with weak transcriptional signatures. These findings support inferred HubmiRs as a biologically informed recoding of transcriptomic data for perturbational drug modeling, while leaving recovery of measured perturbational miRNA responses to further validation.

bioinformatics↗