Biology subjects

Hao, R.

Publications and source records attributed to Hao, R..

9 recordsLinked to original sources

bioRxiv2025

NSUN2-dependent 5-methylcytosine Modification Regulates Influenza A virus Gene Expression and Genomic Packaging

Emerging evidence indicates that methyltransferase NSUN2 catalyzes 5-methylcytosine (m5C) modifications on various viral RNAs and plays important roles in viral biology. However, the regulatory roles of NSUN2 in influenza A virus (IAV) replication have not been elucidated. Here, we revealed that NSUN2 negatively regulated the viral RNA transcription and protein production by knocking out and over-expressing NSUN2. By m5C MeRIP-seq and RNA-BisSeq, NSUN2-dependent m5C sites were identified on both the plus and minus viral RNA strands. In NSUN2-KO cells, the m5C modification on vRNAs was reduced, resulting in the production of a large number of deficient interfering particles (DIPs) which had lower vRNA content, imbalanced genome fragments, abnormal morphology and reduced pathogenicity. Mutation of m5C sites at the 5 and 3 ends of PB2 vRNA interfered with the selective packaging of the 8 vRNA segments into virus particles, resulting in the formation of a variety of abnormally packaged virus particles. PB2-vRNA mutants also had reduced replication ability and pathogenicity in mice. Overall, these data demonstrate that the m5C residues catalyzed by NSUN2 are required on vRNAs for the proper assembly of infectious viral particles, suggesting the depletion of m5C modification as a potential strategy that can be utilized to attenuate IAV strains. Significance StatementInfluenza A virus (IAV) infections pose a significant threat to global public health by causing substantial morbidity and mortality. The segmented nature of the IAV genome requires precise regulation of the genomic assembly to produce infectious progeny virus particles. In this study, we demonstrate that m5C modification is crucial for the proper assembly of infectious viral particles. The lowered level of m5C modifications on vRNAs leads to the generation of defective interfering particles with reduced replication capacity and pathogenicity. Our data shed new light on the selective packaging mechanism of IAV segmented genome and highlight a potential new strategy for attenuating IAV strains by targeting the m5C modification machinery.

microbiology↗

bioRxiv2024

Natural genetic and transcriptomic variation in photosynthesis associated pathways contribute to adaptive traits variation in worldwide Arabidopsis thaliana population

Photosynthesis is the most important reaction underlying carbon fixation. Despite its potential in boosting carbon assimilation, nature variations underlying genes in photosynthesis pathway and their role in adaptive traits variation remains elusive. In this study, we investigated the genetic, transcriptomic variation of 1103 genes in photosynthesis associated pathways, including 82 photosynthesis core genes, 24 plastid-encoded RNA polymerase related genes, 2 nucleus-encoded RNA polymerase-related genes, 34 photomorphogenesis-related genes, 40 genes involved in transcription and translation (TAC) and 938 other nuclear-encoded chloroplast-targeted genes. By de novo assembling the chloroplast genomes of 28 representative accessions and leveraging whole-genome, transcriptome sequencing data from the 1001 Genome Project, we revealed extensive natural genetic and transcriptome variations these genes in worldwide Arabidopsis thaliana population. 34.0% of them were identified with regulatory variations in expression quantitative locus mapping (eQTL) mapping, including key components of Rubisco (RBCS1B, RBCS2B), and Rubisco activase (RCA). Genome-wide and transcriptome-wide association analysis (GWAS/TWAS) showed that these genetic and transcriptomic variations made considerable contribution to variation of adaptive traits. Overall, our study provides insight into the natural genetic variation of these genes among worldwide Arabidopsis thaliana accessions and their role in complex traits variation and adaptation.

plant biology↗

bioRxiv2024

The gut contractile organoid: a novel model for studying the gut motility regulated by coordinating signals between interstitial cells of Cajal and smooth muscles

The gut undergoes peristaltic movements regulated by intricate cellular interactions. How these interactions emerge in the developing gut remains poorly explored due to a lack of model system. We here developed a novel contractile organoid that is derived from the muscle layer of chicken embryonic hindgut. The organoid contained smooth muscle cells (SMCs) and interstitial cells of Cajal (ICCs; pacemaker) with few enteric neurons, and underwent periodic contractions. The organoid was formed by self-organization with morphological arrangements of ICCs (internal) and SMCs (peripheral), allowing identification of these cells in live. GCaMP-Ca2+ imaging analyses revealed that Ca2+ transients between ICC-ICC, SMC-SMC or SMC-ICC were markedly coordinated. Pharmacological studies further suggested a role of gap junctions in ICC-to-SMC signaling, and also possible mechanical feedback from SMCs contraction to ICCs pace-making activities. In addition, two organoids with different rhythm became synchronized when mediated by SMCs, unveiling a novel contribution of SMCs to ICCs pace-making. The gut contractile organoid developed in this study offers a useful model to understand how the rhythm coordination between/among ICCs and SMCs is regulated and maintained during gut development.

developmental biology↗

bioRxiv2023

Comprehensive analyses of 1771 transcriptome from seven tissues enhance genetic and biological interpretations of maize complex traits

By analyzing 1771 RNA-seq datasets from seven tissues in a maize diversity panel, we explored the landscape of multi-tissue transcriptome variation and evolution patterns of tissue-specific genes, and built a comprehensive multi-tissue gene regulation atlas to understand the genetic regulation of maize complex trait. Using transcriptome-wide association analysis, we linked tissue-specific expression variation of 45 genes to variation of 11 agronomic traits. Through integrative analyses of tissue-specific gene regulatory variation with genome-wide association studies, we detected relevant tissue types and candidate genes for a number of agronomic traits, including leaf during the day for anthesis-silking interval (GRMZM2G093210), leaf during the day for kernel Zeinoxanthin level (GRMZM2G143202), and root for ear height (GRMZM2G700665), highlighting the contribution from tissue-specific gene expression to variation of agronomic trait. Our findings provide novel insights into the genetic and biological mechanisms underlying complex traits in maize, and the multi-tissue regulatory atlas serves as a primary source for biological interpretation, functional validation, and genomic improvement of maize.

genetics↗

bioRxiv2023

Polygenic basis of strong and rapid flowering time response to environment perturbations in wild Arabidopsis thaliana population

Despite the importance in understanding the impact of climate change, the genetics of rapid response to changing environments and its role in adaptive evolution remains elusive. Here, we studied flowering time response to environment changes using 514 Arabidopsis thaliana worldwide accessions with re-sequencing genomes and flowering time measurements from ten unique environments with variable temperature, drought, daylight and competition stresses. We revealed a polygenic basis of flowering time mean and plasticity, underpinned by 52 mean and plasticity QTL. Widespread interaction between mean QTL, polygenic background and surrounding environments considerably altered the amount of additive genetic variance and allelic effects of detected QTL. This caused variability in phenotype plasticity and across environment variation in genetic variance, resulting in rapid flowering time response to environment perturbations. In addition, the plastic alleles showed a higher correlation with the environment factors than that from randomly sampled alleles, suggesting a potential role in climate adaptation. We therefore proposed a polygenic interaction model, whereby large effect QTL and polygenic background simultaneously interacted with the surrounding environment, underlying rapid response to changing environments. Results from our study thus provided deeper insights into the genetics of plasticity, with potential benefit in genomic selection of crops in heterogeneous environments and predicting changes in species distribution and the evolutionary trajectory of wild populations.

genetics↗

bioRxiv2023

Enhancing anti-gastrointestinal cancer activities of CLDN18.2 CAR-T armored with novel synthetic NKG2D receptors Containing DAP10 and DAP12 signaling domains.

Chimeric antigen receptor (CAR) T therapies have shown remarkable efficacy in hematopoietic malignancies, but their therapeutic benefits in solid tumors have been limited due to heterogeneities in both antigen types and their expression levels on tumor cells. NK group 2 member D ligands (NKG2DLs) are extensively expressed on various tumors and absent on normal tissues, making them a promising target for cellular immunotherapy. DAP10 and DAP12 function as adaptor proteins in NK cells to transduce activating signals, and recent studies have revealed DAP10 and DAP12s additional role as a co-stimulatory signal in T cells. Our pre-clinical data showed that CAR-T targeting CLDN18.2 is highly effective in gastrointestinal (GI) cancers, but the heterogeneous expression of CLDN18.2 poses a treatment challenge. To complement this antigen deficiency, we demonstrated that NKG2DLs were extensively expressed in GI tumor tissues and formed an ideal dual target. Here, we reported a CLDN18.2 CAR design armored with synthetic NKG2D receptors (SNR) containing DAP10 and DAP12 signaling domains. This novel CAR-T showed improved cytotoxicity against tumor cells with heterogeneous expression of CLDN18.2. The possible underlined mechanism is that SNR promotes CAR-T memory formation and reduces their exhaustion, while also enhancing their expansion and ability to infiltrate immune-excluded tumors in vivo. Taken together, SNR with DAP10/12 signaling and their synergistic involvement, increased CAR-T function and overcame the antigen deficiency, providing a novel treatment modality for solid GI tumor.

immunology↗

bioRxiv2022

Deciphering the conformations and dynamics of FG-nucleoporins in situ

The [~]120 MDa nuclear pore complex (NPC) acts as a gatekeeper for the molecular traffic between the nucleus and the cytosol. Small cargo readily passes through the transport channel, yet large cargo requires specialized nuclear transport receptors. While the scaffold structure that anchors the NPC in the double-layered nuclear envelope has been resolved to remarkable details, the spatial organization of intrinsically disordered nucleoporins (NUPs) within the central channel remains enigmatic. These so-called FG-NUPs account for about one-third of the total mass of the NPC and form the actual transport barrier. Here we combined site-specific fluorescent labeling in non-fixed cells and fluorescent lifetime imaging microscopy (FLIM) to directly decipher the conformations of an essential constituent of the permeability barrier, NUP98, inside the functioning NPCs using Fluorescence resonance energy transfer (FRET). With detailed measurements of the distance distribution of eighteen NUP98 segments combined with coarse-grained modeling, we mapped the uncharted biochemical environment inside the nanosized transport channel. We found that good-solvent conditions for a polymer dominate the inside of the nanosized NPC, expand the FG-domain in situ and facilitate nuclear transport, in sharp contrast to the collapsed NUP98 FG-chain in aqueous solution. The combination of fluorescence microscopy, high-resolution electron tomography, and molecular simulation opens a window into the so-far unresolved organization of the FG-NUPs at the center of NPC function, allowing us to reconcile scientific models of nuclear transport.

biophysics↗

bioRxiv2020

Extra-hypothalamic oxytocin neurons drive stress-induced social vigilance and avoidance

Oxytocin increases the salience of both positive and negative social contexts and it is thought that these diverse actions on behavior are mediated in part through circuit-specific action. This hypothesis is based primarily on manipulations of oxytocin receptor function, leaving open the question of whether different populations of oxytocin neurons mediate different effects on behavior. Here we inhibited oxytocin synthesis in a social stress-sensitive population of oxytocin neurons specifically within the medioventral bed nucleus of the stria terminalis (BNSTmv). Oxytocin knock-down prevented stress-induced increases in social vigilance and decreases in social approach. Viral tracing of BNSTmv oxytocin neurons revealed fibers in regions controlling defensive behaviors including lateral hypothalamus, anterior hypothalamus, and anteromedial BNST (BNSTam). Oxytocin infusion into BNSTam in stress naive mice increased social vigilance and reduced social approach. These results show that a population of extra-hypothalamic oxytocin neurons play a key role in controlling stress-induced social anxiety behaviors.

neuroscience↗

bioRxiv2019

Chromosome level draft genomes of the fall armyworm, Spodoptera frugiperda (Lepidoptera: Noctuidae), an alien invasive pest in China

The fall armyworm (FAW), Spodoptera frugiperda (J.E. Smith) is a severely destructive pest native to the Americas, but has now become an alien invasive pest in China, and causes significant economic loss. Therefore, in order to make effective management strategies, it is highly essential to understand genomic architecture and its genetic background. In this study, we assembled two chromosome scale genomes of the fall armyworm, representing one male and one female individual procured from Yunnan province of China. The genome sizes were identified as 542.42 Mb with N50 of 14.16 Mb, and 530.77 Mb with N50 of 14.89 Mb for the male and female FAW, respectively. We predicted about 22,201 genes in the male genome. We found the expansion of cytochrome P450 and glutathione s-transferase gene families, which are functionally related to the intensified detoxification and pesticides tolerance. Further population analyses of corn strain (C strain) and rice strain (R strain) revealed that the Chinese fall armyworm was most likely invaded from Africa. These strain information, genome features and possible invasion source described in this study will be extremely important for making effective strategies to manage the fall armyworms.

genomics↗