Biology subjects

WANG, H.

Publications and source records attributed to WANG, H..

16 recordsLinked to original sources

bioRxiv2026

Evaluating the added value of sequence models in noncoding RNA assays: a baseline-aware framework

Sequence models are evaluated against non-coding RNA assay read-outs, but prediction alone does not show what their features add to an explicit baseline. We estimated model-added-last changes in AUROC for lncRNA labels and cross-validated Spearman correlation for miRNA repression, fixing members and chromosome folds across available sources. In cross-cell CRISPRi (n = 2961), AlphaGenome increased AUROC from 0.6426 to 0.7551; adding K562 accessibility changed these values to 0.7282 and 0.7534. Corrected-source Cas13 increments ranged from -0.0161 to +0.0130 (n = 871). Separate post-audit comparisons tested fixed sequence composition, broader regularization and TargetScan aggregate identity. With expanded regularization, composition improved four baselines but reduced Cas13 AUROC by 0.0365. RNA-FM's increment was -0.0014 for CRISPRi and +0.000044 for HEK293FT after composition adjustment; small signs changed with regularization. On the same 1227 HeLa members, replacing a seed-family aggregate with an identity-supported mature-miRNA aggregate increased baseline Spearman from 0.4140 to 0.4799. RNA-FM then added 0.0170, or 0.0014 after composition adjustment. These source-row aggregates lack experimental transcript/site alignment. The results support testing baseline content, identity and regularization before interpreting residual model increments. Negative or near-zero increments do not establish absent information or equivalence. Resampling summaries remain conditional descriptions or non-joint sensitivities; calibrated confirmation, justified practical-size thresholds and pretraining-overlap verification were unavailable.

bioinformatics↗

bioRxiv2026

Pharmacological Effects and Candidate Bioactive Constituents of Huanglian Wendan Decoction in Experimental Metabolic Syndrome: Multi-Omics Analysis of Gut-Liver Metabolism and NLRP3 Signaling

Background: Chronic low-grade inflammation and gut microbiota dysbiosis contribute to metabolic syndrome (MS). Huanglian Wendan Decoction (HLWDD) is a defined multi-herbal formulation used in Chinese medicine, but its effects on gut microbiota-associated metabolism and NLRP3 inflammasome signaling remain unclear. Objective: This study evaluated the pharmacological effects and candidate absorbed bioactive constituents of HLWDD in experimental MS. Methods: A high-fat, high-sugar diet-induced rat model of MS was assessed using metabolic, biochemical, histological, molecular, and multi-omics endpoints. Gut metagenomics, untargeted metabolomics of liver and colonic contents, liver transcriptomics, and UPLC-HRMS/MS analysis of serum-absorbed constituents were integrated with network pharmacology and molecular docking. Baicalin was further evaluated in PA-BSA-treated HepG2 cells. Results: HLWDD ameliorated obesity, dyslipidemia, hepatic steatosis, and systemic inflammation and attenuated NLRP3 inflammasome-related signaling. Multi-omics analysis identified nine shared differential metabolites and a strong positive association between Faecalibacterium and butyrate. Thirty-two serum-absorbed constituents were tentatively identified. Baicalin showed favorable predicted interactions with NLRP3 (-5.82 kcal/mol) and CASP1 (-5.41 kcal/mol) and concentration-dependently suppressed NLRP3 inflammasome-related signaling in HepG2 cells; the highest concentration increased intracellular butyrate. Conclusion: HLWDD ameliorated metabolic and inflammatory abnormalities in experimental MS in association with restoration of gut-liver metabolic homeostasis and attenuation of NLRP3 inflammasome signaling. Baicalin emerged as a candidate absorbed bioactive constituent.

systems biology↗

bioRxiv2026

HDA6-mediated histone deacetylation restricts premature tapetal PCD to maintain male fertility during early flowering in Arabidopsis

Histone deacetylation regulates plant development, yet its role in male gametophyte development and fertility remains unclear. Here, we show that histone deacetylase 6 (HDA6), an RPD3-like histone deacetylase, epigenetically regulates timely tapetal programmed cell death (PCD) and male fertility, predominantly during early flowering in Arabidopsis. Loss of HDA6 in axe1-4 causes early-stage male sterility followed by fertility recovery, accompanied by premature tapetal PCD, impaired pollen development and defective pollen wall formation. HDA6 interacts with squamosa promoter binding protein-like 8 (SPL8) to repress Arabidopsis NAC domain containing protein 087 (ANAC087) through H3K9/K14 deacetylation. In axe1-4, ANAC087 derepression activates cysteine endopeptidase 1 (CEP1), triggering precocious tapetal PCD. Genetic suppression of ANAC087 or CEP1 restores male fertility. Thus, HDA6-SPL8 establishes a stage-dependent epigenetic checkpoint that restrains the ANAC087-CEP1 cell death pathway and ensures timely tapetal PCD. Our study reveals how chromatin regulation integrates with developmental timing to safeguard plant male fertility.

plant biology↗

bioRxiv2025

Spatial proximity sequencing maps developmental dynamics in the germinal center

Spatial profiling of proteins and protein interactions is essential for immunology, signaling, development, and cancer. We present Spatial Proximity-Sequencing (Sprox-seq), a multi-omic technique that simultaneously measures proteins, protein complexes and mRNAs, where location of each molecule is also recorded. Sprox-seq profiled 32 proteins, 528 pairwise protein interactions and thousands of mRNAs across human tonsil tissues and germinal centers. Mapping protein interactions recapitulated RNA-defined tissue architecture in germinal centers, but also revealed much higher interaction complexity in the Light zone. Developmental trajectories inferred from protein interactions uncovered a B cell maturation pathway distinct from that inferred by RNA. Integrated protein-complex and mRNA analysis related spatially-enriched complexes with immune regulation and mitotic gene-expression pathways. Furthermore, Sprox-seq captured B cell-Follicular Dendritic Cell interactions mediated by the protein complex VLA-4-VCAM1 in the Light zone. Sprox-seq provides a multi-modal view of cell states and a powerful tool for studying protein and cellular interactions across tissues.

immunology↗

bioRxiv2025

Nanopore direct-RNA sequencing reveals TGEV epitranscriptomic and transcriptomic landscapes modulated by gene 7

Viral non-structural proteins have gained increasing attention for their roles in regulating host-virus interplay and reported to act as a key mediator of host and virus RNA modification dynamics. Transmissible gastroenteritis virus (TGEV) gene 7 has been implicated in virulence, but its other molecular functions remain unclear. Here, we compared wild-type TGEV (TGEV-wt) with a recombinant strain lacking gene 7 (TGEV-{Delta}7) in swine testis cells using Oxford Nanopore direct RNA sequencing. High-coverage datasets enabled simultaneous profiling of the full-length transcriptome, N6-methyladenosine (m6A) modifications, and polyA tail length. Deletion of TGEV gene 7 halved viral RNA replication yet increased m6A modification by [~]32 % across the viral genome, and elevated host m6A levels by [~]17 %, accompanied by reciprocal shifts in the m6A regulators FTO (eraser) and RBM15 (writer). Despite bulk transcriptome changes were comparable between strains, gene 7 deletion introduced additional DEGs beyond WT infection, showing stronger enrichment of antiviral and chemokine pathways, indicating heightened innate immunity. PolyA analysis uncovered the polyA features of TGEV gRNA and sgRNAs, and revealed a gene 7 dependent extension of viral by 7 nt, but not host polyA tails. These findings highlight RNA-modification machinery as a potential target for coronavirus control and provide a framework for vaccine strategies exploiting gene 7 attenuation.

microbiology↗

bioRxiv2025

Reinforcement Learning Identifies Age-Related Balance Strategy Shifts

Falls are one of the leading causes of non-disease death and injury in the elderly, partly due to the loss of muscle mass in a musculoskeletal disorder named sarcopenia. Studying the impact of this muscle weakness on standing balance through direct human experimentation poses ethical dilemmas, involves high costs, and fails to fully capture the internal dynamics of the muscle. To address these limitations, we employ neuromusculoskeletal modeling to explore the impact of sarcopenia on balance. In this study, we introduce a novel full-body musculoskeletal model comprising both the torso and lower limbs, with 290 muscle actuators controlling 23 degrees of freedom and supporting varying levels of sarcopenia. Using reinforcement learning coupled with curriculum learning and muscle synergy representations, we trained an agent to perform standing balance on a backward-sliding plate and compared its behavior to human experiments. Our results demonstrate that, without pre-recorded experimental data, both healthy and sarcopenic agents can reproduce ankle and hip balancing strategies consistent with experimental findings. Furthermore, we show that as the degree of sarcopenia increases, the agent adapts its balancing strategy based on the platforms acceleration.

bioengineering↗

bioRxiv2025

MyoBack: A Musculoskeletal Model of the Human Back with Integrated Exoskeleton

Given the challenges of real-life experimentation, musculoskeletal simulation models could become essential in biomedical research. This is especially critical for the human back, a key structure involved in daily movements, where modeling and simulation could streamline design and support the development of treatments and robotic rehabilitation techniques, such as exoskeletons. However, musculoskeletal simulation engines are computationally demanding and lack contact dynamics, restricting current models use in studying prolonged behaviors or optimizing system design while maintaining physiological accuracy. To overcome this limitation, this work proposes MyoBack, a human back model part of the MyoSuite framework relying on the physics engine MuJoCo. This model is derived from a physiologically accurate model built in the state-of-the-art musculoskeletal simulation software OpenSim and replicates the latters kinematic properties accurately, with some discrepancies regarding muscle dynamics stemming from engine differences. The MyoBack model was also validated empirically by integrating a passive back exoskeleton in simulation and comparing forces exerted on the back with values from experimental trials. Over different tasks, the model reproduced measured force progressions well, resulting in RMSE = 11% for a stoop and RMSE = 16% for a squat motion pattern relative to peak forces. The MyoBack model can be accessed here: https://github.com/rohwalia/MyoBack

bioengineering↗

bioRxiv2025

Charting Postnatal Heart Development Using In Vivo Single-Cell Functional Genomics

The transition at birth, marked by increased circulatory demands and rapid growth, necessitates extensive remodeling of the hearts structure, function, and metabolism. This transformation requires precise spatial and temporal coordination among diverse cardiac cell types; central to this process is cardiomyocyte maturation, yet the regulatory mechanisms driving these changes remain poorly understood. Here, we present a temporal and spatial atlas of postnatal hearts by integrating single-nucleus transcriptomics with image-based spatial transcriptomics, which uncovers the dynamic regulatory networks of cardiomyocyte maturation. To functionally interrogate candidate regulators in vivo, we developed Probe-based Indel-detectable Perturb-seq (PIP-seq), a high-throughput platform that uses probe-based chemistry to directly capture sgRNA expression, perturbation status, and transcriptomic profiles at single-nucleus resolution. Applying PIP-seq to postnatal cardiac development identified 21 novel regulators of cardiomyocyte maturation, highlighting critical nodal points in this process. Our study establishes a high-resolution framework for dissecting postnatal heart development, underscoring the integrative and highly ordered roles of microenvironment and intercellular communication in cardiomyocyte maturation. Importantly, PIP-seq enables systematic, high-throughput exploration of gene function and networks underlying complex biological processes in their native in vivo context.

developmental biology↗

bioRxiv2025

NtLLG4-mediated unconventional polar exocytosis of NtPPME1 coordinates cell wall rigidity and membrane dynamics to control pollen tube integrity

Plant fertilization relies on controlled pollen tube growth that integrates membrane dynamics and cell wall expansion. We previously identified an unconventional exocytic pathway wherein Golgi-derived secretory vesicles (GDSVs) bypass the trans-Golgi network to deliver Nicotiana tabacum pectin methylesterase 1 (NtPPME1), thereby modulating cell wall rigidity. However, the mechanisms linking this patwhay with membrane dynamics and signaling remain elusive. Here, we used cryo-FIB-SEM and 3D tomography to identified GDSVs as a distinct vesicle population at the pollen tube tip. We further demonstrated that tobacco LORELEI-like-GPI-anchored protein 4 (NtLLG4), a key signaling molecule controlling membrane dynamics and integrity, functions as a receptor for NtPPME1, regulating its polar exocytosis via GDSVs to control cell wall stiffness. Furthermore, we identified trafficking signals which direct the unconventional exocytosis of NtPPME1 across intracellular organelles. Our findings reveal a crucial mechanism coupling cell wall rigidity with membrane signaling to control pollen tube growth and integrity during fertilization. TeaserWe reveal a mechanism coupling cell wall rigidity with member signaling to control pollen tube growth and integrity during plant fertilization.

plant biology↗

bioRxiv2024

The fully activated open state of KCNQ1 controls the cardiac 'fight-or-flight' response

The cardiac KCNQ1+KCNE1 (IKs) channel regulates heart rhythm in both normal and stress conditions. Under stress, the {beta}-adrenergic stimulation elevates the intracellular cAMP level, leading to KCNQ1 phosphorylation by protein kinase A and increased IKs, which shortens action potentials to adapt to accelerated heart rate. An impaired response to the {beta}-adrenergic stimulation due to KCNQ1 mutations is associated with the occurrence of a lethal congenital long QT syndrome (type 1, also known as LQT1). However, the underlying mechanism of {beta}-adrenergic stimulation of IKs remains unclear, impeding the development of new therapeutics. Here we find that the unique properties of KCNQ1 channel gating with two distinct open states are key to this mechanism. KCNQ1s fully activated open (AO) state is more sensitive to cAMP than its intermediate open (IO) state. By enhancing the AO state occupancy, the small molecules ML277 and C28 are found to effectively enhance the cAMP sensitivity of the KCNQ1 channel, independent of KCNE1 association. This finding of enhancing AO state occupancy leads to a potential novel strategy to rescue the response of IKs to {beta}-adrenergic stimulation in LQT1 mutants. The success of this approach is demonstrated in cardiac myocytes and also in a high-risk LQT1 mutation. In conclusion the present study not only uncovers the key role of the AO state in IKs channel phosphorylation, but also provides a new target for anti-arrhythmic strategy. Significance statementThe increase of IKs potassium currents with adrenalin stimulation is important for "fight-or-flight" responses. Mutations of the IKs channel reducing adrenalin responses are associated with more lethal form of the type-1 long-QT syndrome (LQT). The alpha subunit of the IKs channel, KCNQ1 opens in two distinct open states, the intermediate-open (IO) and activated-open (AO) states, following a two-step voltage sensing domain (VSD) activation process. We found that the AO state, but not the IO state, is responsible for the adrenalin response. Modulators that specifically enhance the AO state occupancy can enhance adrenalin responses of the WT and LQT-associated mutant channels. These results reveal a mechanism of state dependent modulation of ion channels and provide an anti-arrhythmic strategy.

biophysics↗

bioRxiv2022

DeDoc2 identifies and characterizes the hierarchy and dynamics of chromatin TAD-like domains in the single cells

Topologically associating domains (TAD) are functional chromatin units with hierarchical structure. However, the existence, prevalence and dynamics of such hierarchy in single cells remain unexplored. Here, we report a new generation TAD-like domain (TLD) detection algorithm, named deDoc2, to decode the hierarchy of TLDs in single cells. With dynamic programming, deDoc2 seeks genome partitions with global minimal structure entropy for both whole and local contact matrix. Compared to state-of-the-art tools, deDoc2 can uniquely identify the hierarchy of TLDs in single cells, in addition to outperforming its competitors. By applying deDoc2, we showed that the hierarchy of TLDs in single cells is highly dynamic during cell cycle, as well as among human brain cortex cells, and that it is associated with cellular identity and functions. Thus, our results demonstrated the abundance of information potentially encoded by TLD hierarchy for functional regulation. The deDoc2 can be freely accessed at https://github.com/zengguangjie/deDoc2.

bioinformatics↗

bioRxiv2022

ATG5- and ATG7-mediated autophagy regulates pollen tube guidance and male fertility in Arabidopsis thaliana

Autophagy functions as a crucial cellular scavenger by targeting cytoplasmic cargo to specific lysosome/vacuole for degradation. Autophagy-related (ATG) core proteins including ATG5 and ATG7 are evolutionarily conserved factors that are spatiotemporally orchestrated to regulate multiple processes of autophagy in yeast, mammalian and plant cells. However, autophagy is believed to be functionally dispensable in Arabidopsis thaliana since severe defects during plant growth, development and reproduction have not been observed in most of the ATG loss-of-function mutants, including atg5 and atg7, under standard cultivation conditions. In this study, we report that autophagy does in fact play roles in regulating pollen tube growth guidance and male fertility in Arabidopsis thaliana. A detailed re-assessment of atg5 and atg7 mutants revealed greatly reduced autophagy activity in germinated pollens and the seed formation within siliques is partially abolished. Next, we demonstrated that both the pollen germination ratio and pollen tube length of the mutants decreased at the beginning of germination by time-lapse tracking of pollen germination in vitro and in vivo. Additionally, we observed occurrences of pollen tube twisting and stacking during their growth towards the ovules. Finally, we found abnormal pollen grains containing only a single sperm cell or an undivided generative nucleus. Collectively, these results indicate that ATG5- and ATG7-mediated autophagy is functionally involved in regulating pollen germination, tube growth guidance and sperm cell development in Arabidopsis thaliana.

plant biology↗

bioRxiv2022

A Chromosome-level Assembly of the Japanese Eel Genome, Insights into Gene Duplication and Chromosomal Reorganization

AO_SCPLOWBSTRACTC_SCPLOWJapanese eels (Anguilla japonica) are commercially important species that have been harvested extensively for foods. Currently, this and related species (American and European eels) are difficult to breed on a commercial basis. Wild stock is used for aquaculture. Due to pollution, overfishing, and international trafficking, eel populations are declining. The International Union for Conservation of Nature lists Japanese eels as critically endangered and on its red list. Here we presented a high-quality genome assembly for Japanese eels and demonstrated that large chromosome reorganizations occurred in the events of third-round whole-genome duplications (3R-WRD). Following multiple chromosomal fusion and fission rearrangement, the Anguilla lineage has reduced the haploid chromosomal number of 19 from the ancestral proto-chromosomal number of 25. Phylogenetic analysis of expanded gene families showed the gene families of olfactory receptors and voltage-gated Ca2+-channel expanded significantly. The expansion of olfactory receptors (group {delta} and {zeta} genes) and voltage-gated Ca2+-channel gene families are important for olfaction and neurophysiological functions. Following 3R-WGD, additional tandem (TD) and proximal (PD) duplications occurred to acquire immune-related genes for adaptation. The Japanese eel assembly presented here can be used to study other Anguilla species that are related to evolution and conservation.

genomics↗

bioRxiv2020

Formation of an Aminovinyl-Cysteine Residue in Thioviridamide Non-Lanthipeptides Occurs through a Path Independent of Known Lanthionine Synthetase Activity in Streptomyces sp. NRRL S-87

2-Aminovinyl-cysteine (AviCys) is an unusual thioether amino acid shared by a variety of ribosomally synthesized and posttranslationally modified peptides (RiPPs), as part of a macrocyclic ring system that contains the C-terminal 4 or 6 residues of a precursor peptide. This amino acid is nonproteinogenic and arises from processing the C-terminal Cys residue and an internal Ser/Thr residue to form an unsaturated thioether linkage. Enzyme activities for forming lanthionine (Lan), a distinct saturated thioether residue characteristic of lanthipeptide-related RiPPs, has long been speculated to be necessary for AviCys formation. Based on investigations into the biosynthesis of thioviridamide non-lanthipeptdes in Streptomyces sp. NRRL S-87, we here report an alternative path for AviCys formation that is independent of known Lan synthetase activity. This path relies on four dedicated enzymes for posttranslational modifications of the precursor peptide, in which TvaES-87, a phosphotransferase homolog, plays a critical role. It works with LanD-like flavoprotein TvaFS-87 to form a minimum AviCys synthetase complex that follows the combined activity of TvaCDS-87 for Thr dehydration and catalyzes Cys oxidative decarboxylation and subsequent Michael addition of the resulting enethiol nucleophile onto the newly formed dehydrobutyrine residue for cyclization. With TvaES-87, TvaFS-87 activity for Cys processing can be coordinated with TvaCDS-87 activity for minimizing competitive or unexpected spontaneous reactions and forming AviCys effectively.

biochemistry↗

bioRxiv2020

Lanthipeptide Synthetases Participate the Biosynthesis of 2-Aminovinyl-Cysteine Motifs in Thioamitides

Thioamitides are a group of ribosomally synthesized and post-translational modified peptides with potent antiproliferative and pro-apoptotic activities. Their biosynthesis remains largely unknown, especially for the characteristic C-terminal 2-aminovinyl-Cysteine (AviCys) motifs. Herein, we report the discovery that homologs of class III lanthipeptide synthetases (LanKCts)encoded outside putative thioamitide biosynthetic gene clusters (BGCs) fully dehydrate the precursor peptides. Remarkably, LanKCt enzymes bind tightly to cysteine decarboxylases encoded inside thioamitide BGCs, and the resulting complex complete the macrocyclization of AviCys rings. Furthermore, LanKCt enzymes are present in the genomes of many thioamitide-producing strains and are functional when in complex with cysteine decarboxylases to produce AviCys macrocycles. Thus, our study reveals the participation of lanthipeptide synthetases as a general strategy for dehydration and AviCys formation during thioamitides biosynthesis and thus paves the way for the bioengineering of this class of bioactive natural products.

biochemistry↗

bioRxiv2019

In Vivo Study of Key Transcription Factors in Muscle Satellite Cells by CRISPR/Cas9/AAV9-sgRNA Mediated Genome Editing

Skeletal muscle satellite cells (SCs) are adult muscle stem cells responsible for injury induced muscle regeneration. Despite advances in the knowledge of molecular mechanisms regulating SC lineage progression, our understanding of key transcription factors (TFs) and their regulatory functions in SCs in particularly the quiescent and early activation stages remains incomplete due to the lack of efficient method to screen and investigate the stage-specific key TFs. In this study, we succeeded in defining a distinct list of key TFs in early stages of SC fate transition using the paradigm of super enhancers (SEs). Particularly, leveraging the Cre-dependent Cas9 knockin mice and AAV9 mediated sgRNAs delivery, we generated a facile muscle specific genome editing system which allows gene depletion in SCs in vivo. Using MyoD locus as a proof of concept, we demonstrated that this CRISPR/Cas9/AAV9-sgRNA system can efficiently introduce mutagenesis at target locus and recapture the phenotypes reported in knockout mice. Further application of the system on key TFs, Myc, Bcl6 and Pknox2, revealed their distinct functions in the early stage of SC activation and damage induced muscle regeneration. Altogether our findings have proven the CRISPR/Cas9/AAV9-sgRNA system as a robust way for in vivo genome editing and elucidation of key factors governing SC activities.

genetics↗