Biology subjects

Wang, M. H.

Publications and source records attributed to Wang, M. H..

7 recordsLinked to original sources

bioRxiv2025

Genome-wide Viral Nascent RNA Sequencing Unveils Polymerase Pausing Landscape at Single-nucleotide Precision

Understanding viral replication and transcription mechanisms is critical for developing effective antiviral strategies. The study of viral gene regulation in host cellular environment is an important bridge for translating mechanistic discoveries from in vitro studies to in vivo but it remains stagnated due to the absence of technological advancement. Current methods for studying viral transcription and replication have been limited to capturing only the mature viral RNAs, obscuring the dynamic intermediates and mechanistic details of these crucial processes. Here, we introduce an original technology we called "Total Elongating Nascent VIral Polymerase single-molecule Sequencing (TenVIP-seq)", which isolates and analyses newly synthesized RNA within the viral RNA-dependent RNA polymerase (RdRp) complex, enabling the discovery of mechanisms critical for both viral replication and transcription. Our first characterization of nascent RNA species for an RNA virus showed that RdRP exhibited non-random pausing with profile signatures along the eight influenza A virus (IAV) gene segments. We also revealed genome-wide pausing at known regulatory sites, such as the poly(U) tract polyadenylation site, and new putative regulatory sites at single-nucleotide resolution. Distinct pausing features between the viral genomic (vRNA) and anti-genomic (cRNA/mRNA) templates were observed, suggesting that RdRp processes transcription and replication differentially on positive and negative sense RNA. The NTP analog drug T-705 (favipiravir) intensified RdRp pauses during genome replication and transcription without introducing new pausing sites, while TRIM25 knockout in host cells infected with virus reduced RdRp pausing globally across the viral genome. Strikingly, we observed that terminal nucleotide misincorporations of nascent RNA sequencing of paused RdRP, which were previously undetectable, were as high as an average of 51.6% (vRNA) and 44.0% (cRNA/mRNA), suggesting that the mutational rate of viruses is much higher than previously thought. We demonstrated that TenVIP-seq holds potential in providing insights into the molecular mechanisms that control viral genome replication, gene expression and regulation, mutation, antiviral drug treatment, and virus-host interaction.

genetics↗

bioRxiv2024

An emerging PB2-627 polymorphism increases the pandemic potential of avian influenza virus by breaking through ANP32 host restriction in mammalian and avian hosts

Alterations in the PB2-627 domain could substantially increase the risk of an avian influenza virus (AIV) pandemic. So far, a well-known mammalian mutation PB2-E627K has not been maintained in AIV in poultry, which limits the spread of AIVs from avian to humans. Here, we discovered a variant, PB2-627V, which combines the properties of avian-like PB2-627E and human-like PB2-627K, overcoming host restrictions and posing a risk for human pandemics. Specifically, by screening the global PB2 sequences, we discovered a new independent cluster with PB2-627V emerged in the 2010s, which is prevalent in various avian, mammalian, and human isolates of AIVs, including H9N2, H7N9, H3N8, 2.3.4.4b H5N1, and other subtypes. And, the increasing prevalence of PB2-627V in poultry is accompanied by a rise in human infection cases with this variant. Then we systematically assessed its host adaptation, fitness, and transmissibility across three subtypes of AIVs (H9N2, H7N9, and H3N8) in different host models, including avian and human cells, chickens, mice, and ferrets where infections naturally occur. We found that PB2-627V facilitates AIVs to efficiently infect and replicate in chickens and mice by utilizing both avian- and human-origin ANP32A proteins. Importantly, and like PB2-627K, PB2-627V promotes efficient transmission between ferrets through respiratory droplets. Deep sequencing in passaged chicken samples and transmitted ferret samples indicates that PB2-627V remains stable across the two distinct hosts and has a high potential for long-term prevalence in avian species. Therefore, the mutation has the ability to continue spreading among poultry and can also overcome the barrier between birds and humans, greatly enhancing the likelihood of AIVs infecting humans. Given the escalating global spread of AIVs, it is crucial to closely monitor influenza viruses carrying PB2-627V to prevent a pandemic.

microbiology↗

bioRxiv2023

Predictive evolutionary modelling for influenza virus by site-based dynamics of mutations

A predictive evolutionary model was developed to forecast representative influenza viral strains and select vaccine strains for upcoming epidemic seasons. Influenza virus continuously evolves to escape human adaptive immunity and generates seasonal epidemics. A computational approach beth-1 that models site-wise mutation dynamics demonstrated remarkable matching of predicted strains to the circulating viruses in subsequent seasons for the influenza A(H1N1)pdm09 and A(H3N2) viruses in both retrospective and prospective validations. The method offers a promising and ready-to-use tool to facilitate vaccine strain selection for the influenza virus, achieved by capturing heterogeneous evolutionary dynamics over genome space-time and linking molecular variants to population immune response. One-Sentence SummaryA computational model predicts virus evolution and facilitates vaccine strain selection for the influenza virus

evolutionary biology↗

bioRxiv2022

A Prism Vote Framework for Individualized Risk Prediction of Traits in Genome-wide Sequencing Data of Multiple Populations

Multi-population cohorts offer unprecedented opportunities for profiling disease risk in large samples, however, heterogeneous risk effects underlying complex traits across populations make integrative prediction challenging. In this study, we propose a novel Bayesian probability framework, the Prism Vote (PV), to construct risk predictions in heterogeneous genetic data. The PV views the trait of an individual as a composite risk from subpopulations, in which stratum-specific predictors can be formed in data of more homogeneous genetic structure. Since each individual is represented by a composition of subpopulation memberships, the framework enables individualized risk characterization. Simulations demonstrated that the PV framework applied with alternative prediction methods significantly improved prediction accuracy in mixed and admixed populations. The advantage of PV enlarges as the sample size, genetic heterogeneity, and population diversity increase. In two real genome-wide association data consists of multiple populations, we showed that the framework enhanced prediction accuracy of the linear mixed model by up to 12.1% in five-group cross validations. The proposed framework offers a new aspect to analyze individuals disease risk and improve accuracy for predicting complex traits in genome data.

genetics↗

bioRxiv2020

Temporal patterns in the evolutionary genetic distance of SARS-CoV-2 during the COVID-19 pandemic

BackgroundDuring the pandemic of coronavirus disease 2019 (COVID-19), the genetic mutations occurred in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) cumulatively or sporadically. In this study, we employed a computational approach to identify and trace the emerging patterns of the SARS-CoV-2 mutations, and quantify accumulative genetic distance across different periods and proteins. MethodsFull-length human SARS-CoV-2 strains in United Kingdom were collected. We investigated the temporal variation in the evolutionary genetic distance defined by the Hamming distance since the start of COVID-19 pandemic. FindingsOur results showed that the SARS-CoV-2 was in the process of continuous evolution, mainly involved in spike protein (S protein), the RNA-dependent RNA polymerase (RdRp) region of open reading frame 1 (ORF1) and nucleocapsid protein (N protein). By contrast, mutations in other proteins were sporadic and genetic distance to the initial sequenced strain did not show an increasing trend.

bioinformatics↗

bioRxiv2019

Cell wall integrity signaling regulates cell wall regeneration via transcriptional activation in Chlamydomonas reinhardtii

An intact cell wall is critical for protecting the cell from osmotic challenges and harmful environments. Signaling mechanisms are necessary to monitor cell wall integrity and to regulate cell wall production and remodeling during growth and division cycles. The green alga, Chlamydomonas, has a proteinaceous cell wall of defined structure that is readily removed by gametolysin (g-lysin), a metalloprotease released during sexual mating. Naked cells treated with g-lysin induce the mRNA accumulation of > 100 cell wall-related genes within an hour, offering a system to study signaling and regulatory mechanisms for de novo cell wall assembly. Combining quantitative RT-PCR and luciferase reporter assays to probe transcript accumulation and promoter activity, we revealed that up to 500-fold upregulation of cell wall-related genes was driven at least partly by transcriptional activation upon g-lysin treatment. To investigate how naked cells trigger this rapid transcriptional activation, we tested whether osmotic stress and cell wall integrity are involved in this process. Under a constant hypotonic condition, comparable levels of cell wall-gene activation were observed by g-lysin treatment. In contrast, cells in an iso- or hypertonic condition showed up to 80% reduction in the g-lysin-induced gene activation, suggesting that hypotonic conditions are required for full-scale responses to g-lysin treatment. To test whether mechanical perturbation is involved, we isolated and examined a new set of cell wall mutants with defective or little cell walls. All cell wall mutants examined showed a constitutive upregulation of cell wall-related genes at the level, which would only be achieved by the g-lysin treatment in wild-type cells. Our study suggests a signaling that monitors mechanical defects of cell walls and regulates cell wall-gene expression in Chlamydomonas, which may relate to cell wall integrity signaling mechanisms in plants.

plant biology↗

bioRxiv2018

Common ancestry of heterodimerizing TALE homeobox transcription factors across Metazoa and Archaeplastida

Homeobox transcription factors (TFs) in the TALE superclass are deeply embedded in the gene regulatory networks that orchestrate embryogenesis. Knotted-like homeobox (KNOX) TFs, homologous to animal MEIS, have been found to drive the haploid-to-diploid transition in both unicellular green algae and land plants via heterodimerization with other TALE superclass TFs, representing remarkable functional conservation of a developmental TF across lineages that diverged one billion years ago. To delineate the ancestry of TALE-TALE heterodimerization, we analyzed TALE endowment in the algal radiations of Archaeplastida, ancestral to land plants. Homeodomain phylogeny and bioinformatics analysis partitioned TALEs into two broad groups, KNOX and non-KNOX. Each group shares previously defined heterodimerization domains, plant KNOX-homology in the KNOX group and animal PBC-homology in the non-KNOX group, indicating their deep ancestry. Protein-protein interaction experiments showed that the TALEs in the two groups all participated in heterodimerization. These results indicate that the TF dyads consisting of KNOX/MEIS and PBC-containing TALEs must have evolved early in eukaryotic evolution, a likely function being to accurately execute the haploid-to-diploid transitions during sexual development.\n\nAuthor summaryComplex multicellularity requires elaborate developmental mechanisms, often based on the versatility of heterodimeric transcription factor (TF) interactions. Highly conserved TALE-superclass homeobox TF networks in major eukaryotic lineages suggest deep ancestry of developmental mechanisms. Our results support the hypothesis that in early eukaryotes, the TALE heterodimeric configuration provided transcription-on switches via dimerization-dependent subcellular localization, ensuring execution of the haploid-to-diploid transition only when the gamete fusion is correctly executed between appropriate partner gametes, a system that then diversified in the several lineages that engage in complex multicellular organization.

evolutionary biology↗