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At least 253 records · Page 14Linked to original sources

PubMed2025

Transcriptome-Wide Analysis of the 5' Cap Status of RNA Using 5' Monophosphate-Dependent Exonuclease Digestion and RNA Sequencing.

Eukaryotic mRNAs carry an N7-methylguanosine (m7G) cap structure at their 5' extremity, which protects them from the degradation by 5'-3' exoribonucleases and plays a pivotal role in mRNA metabolism, promoting splicing, nuclear export, and translation. Decapping, the enzymatic process that removes this structure, is a key event during cytoplasmic mRNA 5'-3' decay, leading to the degradation of the transcript body by Xrn1. In this chapter, we describe a procedure to assess the cap status of RNA at the transcriptome level. It is based on a treatment of total RNA extracts with a 5' monophosphate-dependent exonuclease, which like Xrn1 specifically degrades decapped RNAs harboring 5' monophosphate extremities, but not RNAs with intact m7G cap. The digested RNAs are then analyzed by RNA sequencing.

Exoribonucleases↗

PubMed2025

Integrated transcriptomic, transcriptional factors, and protein interaction reveal the regulatory mechanisms of flowering time in rice (Oryza sativa L.).

Appropriate flowering time is important for rice regional adaptation and optimum rice production, but little is known about the omics of heading date in rice. Here, we studied omics including transcriptome, proteome and transcriptional factors to identify regulatory genes related to flowering time. A total of 1402 differentially expressed genes (DEGs, 721 up-regulated and 681 down-regulated) were detected in wild and mutant. These transcripts are classified according to biological processes, cellular components, and molecular functions. Among these differentially expressed genes, many transcription factor genes demonstrated multiple regulatory pathways involved in flowering time. Gene expression analysis showed that Os03g0122600 (OsMADS50), Os08g0105000 (Ehd3), Os06g0275000 (Hd1) were expressed higher and Os06g0199500 (OsHAL3), Os06g0498800 (OsMFT1), Os08g0105000 (Ehd3), Os06g0157700 (Hd3a), and Os02g0731700 (Ghd2), were expressed lower in wild compared to mutant, which are the key genes that regulate the flowering in rice. In addition, Ghd7 interacted with Os10g30860 and Os12g08260 using yeast two-hybrid assay. We identified 28 potential Ghd7 transcriptional regulators using the transcription factor-centered yeast one hybrid (TF-Centered Y1H) assay. Taken together, this study developed a new set of genomic resources to identify and characterize genes, proteins, and motifs associated with flowering time.

Oryza↗

PubMed2026

ScRNA-seq analysis reveals the effects of nitrite stress on the endocrine system of the eyestalk in Litopenaeus vannamei.

Nitrite is a harmful substance generated in Litopenaeus vannamei farming systems, largely originating from the inadequate breakdown of surplus feed and shrimp feces. Its accumulation in the water can affect the growth and physiological functions of shrimp, damage the immune system, and even cause mass mortality, thus becoming a key environmental factor restricting the green development of the industry. Under nitrite stress, the eyestalk, as an important neuroendocrine regulatory center in crustaceans, participates in the stress adaptation of the organism and exerts a protective effect by regulating energy metabolism and immune function. However, the molecular regulatory mechanism of the eyestalk in response to nitrite stress remains unclear. In this study, single-cell RNA sequencing (scRNA-seq) technology was used to analyze the heterogeneity of eyestalk cells in L. vannamei under nitrite stress. A total of 18, 394 high-quality cells were obtained, and six major cell subpopulations, including Neurosecretory cell, Motor neuron, Sensory neuron, Interneuron, Neurogliocyte, and Support cell, were identified. Differential expression analysis identified 839 differentially expressed genes, and different cell types showed distinct specific responses to nitrite stress. Functional enrichment analysis indicated that pathways such as glycolysis, oxidative phosphorylation, ribosome function, and endoplasmic reticulum protein processing were significantly activated, while signal transduction and DNA repair-related pathways were inhibited. Further analysis revealed that nitrite stress could induce mitochondrial function changes and trigger oxidative stress, thereby affecting the neuroendocrine system function of the eyestalk. This study provided insights into transcriptomic responses of the eyestalk to nitrite stress at the single-cell level, laying a theoretical foundation for the management of aquaculture environments.

Animals↗

PubMed2026

Transcriptomic insights into temperature regulation of proliferation and differentiation in skeletal muscle cells of Nibea albiflora.

Myogenesis involves sequential stages of muscle satellite cell activation, myoblast proliferation, differentiation, and fusion into multinucleated myotubes. Teleost muscle exhibits indeterminate growth and is highly sensitive to environmental temperature, yet the underlying mechanisms by which temperature regulate proliferation and differentiation remain poorly understood. In this study, we established a primary skeletal muscle cell culture from the yellow drum (Nibea albiflora), an economically important marine fish, and integrated morphological observations with comparative transcriptomics analysis to characterize cellular and molecular responses at 28 °C and 20 °C during both proliferation and differentiation stages. Phenotypic analysis revealed that 28 °C significantly enhanced both myoblast proliferation and myogenic differentiation ability compared with 20 °C. Transcriptomic profiling revealed that at 28 °C, differentiation upregulated extracellular matrix(ECM) organization, calcium signaling, and sarcomere assembly, while proliferation enhanced focal adhesion, growth factor signaling, and lipid metabolism. At 20 °C, differentiation was characterized by glutathione metabolism, and ferroptosis, while proliferation involved cytokine-cytokine receptor interaction and negative regulation of signal transduction. Core myogenic regulatory factors (MRFs), particularly myogenin, were strongly upregulated at 28 °C during the differentiation stage, serving as an internal control. Based on these findings, we propose a testable model that elevated temperature coordinates Ca2+-dependent MRF activation with ECM-integrin signaling to drive sarcomere assembly and muscle growth. Key differentially expressed genes (DEGs) regulating myogenesis in N. albiflora were also identified. This study provides a mechanistic framework for temperature adaptation in teleost skeletal muscle and identifies candidate genes for functional validation and marker-assisted selection, as well as a rationale for temperature management strategies to improve aquaculture yield of N. albiflora.

Animals↗

PubMed2026

Integrative analysis of transcriptome and DNA methylome dynamics during caudal fin regeneration in silver pomfret (Pampus argenteus).

Caudal fin regeneration in teleost fish is a complex, multi-stage process involving coordinated molecular and cellular changes. While the role of epigenetic regulation particularly DNA methylation has been studied in model freshwater species such as zebrafish, its contribution to regeneration in marine teleosts remains largely unexplored. In this study, we integrated transcriptomic and DNA methylomic data to characterize the temporal dynamics of gene expression and methylation during caudal fin regeneration in the silver pomfret (Pampus argenteus). Using RNA-sequencing and reduced representation bisulfite sequencing (RRBS) at three biologically critical time points 1, 3, and 7 days post-amputation (dpa), we characterized the spatiotemporal molecular landscape of caudal fin regeneration. These time points capture the key transitional phases of wound healing and inflammation (1 dpa), blastema formation and progenitor proliferation (3 dpa), and regenerative outgrowth with tissue remodeling (7 dpa), enabling robust detection of the major molecular programs underlying epimorphic regeneration. Concurrently, CG-methylome analysis identified thousands of dynamically changing differentially methylated regions (DMRs). A strong global inverse correlation was observed between promoter methylation and gene expression. Integrative analysis pinpointed key regeneration genes (fgf20a, msxb, sox9b) whose expression was associated with dynamic methylation changes in their promoters or gene bodies. We conclude that DNA methylation is a dynamic and key regulatory layer that acts in concert with transcriptional reprogramming to coordinate tissue regeneration, providing new insights into the epigenetic mechanisms underlying complex regenerative processes in teleosts.

Animals↗

PubMed2025

Cell-type-specific defense priming and NHP-dependent systemic immunity against Pectobacterium in Chinese cabbage.

Defense priming is an effective strategy for mounting the defensive capacity of plants. Primed plants undergo minimal changes, enabling rapid, robust responses to subsequent pathogen attack. The cell-type-specific mechanisms underlying priming and systemic immunity remain unclear. Using single-nucleus RNA sequencing (snRNA-seq), we reveal how primed Chinese cabbage coordinates N-hydroxypipecolic acid (NHP)-dependent systemic immunity against Pectobacterium carotovorum. NHP accumulates as a phloem-mobile priming signal. snRNA-seq identified a priming-specific epidermal cell state transition and transcriptional cascade: BrWRKY18-1 activates BrWRKY33-1 expression during priming, initiating NHP-dependent systemic immunity. At post-challenge primed state, pathogenesis-related genes (PRs), such as BrPR3, BrPR4-1, and BrPR4-2, are predominantly expressed in systemic tissues to inhibit infection. Notably, the functionality of these PR genes in immunity necessitates their expression in all cells to effectively enhance defensive resistance. This NHP-transcription factor-PR axis couples mobile signaling to systemic immunity, elucidating cell-type-specific defense priming.

Plant Immunity↗

PubMed2026

When light colour matters: Spectral quality is associated with distinct small RNA candidates in Arabidopsis thaliana.

The spectral composition of incident light is perceived by plant photoreceptors and can rapidly reshape downstream gene expression programs; however, its impact on the small-RNA layer beyond annotated miRNAs remains incompletely characterized. The objective of this study was to determine whether 3 h exposure of Arabidopsis thaliana rosettes to blue, green, red, or white light at an equal photosynthetic photon flux density (PPFD) of 400 μmol m-2 s-1 is associated with distinct profiles of candidate small RNAs. A stringent discovery and post-processing workflow was applied to identify high-confidence, treatment-associated small RNA candidates beyond annotated miRNA. The miRkwood-based pipeline, combined with additional filtering and contextual annotation, recovered a compact set of candidates dominated by the blue-light treatment (41 candidates), compared with fewer candidates associated with red (8), green (6), and white light (3). Genomic-context analysis indicated that most candidate sites were intergenic, with candidates detected under green light being entirely intergenic, and overlap with transposon annotations was used to distinguish candidates arising from transposon-rich genomic space. Sequence-feature profiling revealed pronounced treatment-dependent terminal nucleotide biases at both 5' and 3' ends, consistent with spectrum-associated shifts in length-class and terminal-nucleotide signatures that are informative for AGO-loading hypotheses. Target prediction highlighted a subset of genes showing convergent targeting by multiple independent blue-associated candidates, and duplex summaries showed structured, plant-like complementarity patterns (including frequent 10-11 pairing). Together, these results indicate that 3 h exposure to wavelength-defined light at 400 μmol m-2 s-1, particularly blue light, is associated with a distinct profile of detectable candidate small RNAs in Arabidopsis leaves and identify candidate interactions for follow-up validation.

5′ nucleotide bias↗

PubMed2026

Pervasive noise in human pre-mRNA splice site selection.

RNA splicing has historically been thought to be highly efficient and accurate, with little opportunity for deviation from regulated alternative splicing. This dogma has been challenged by recent observations that biological noise may contribute substantially to transcriptome diversity. However, quantitative understanding of stochastic splicing variation is challenging because these transcripts are likely subject to rapid degradation. Here, we use deep sequencing across RNA compartments to track splicing intermediates in human cells and see abundant cryptic splicing associated with genomic features that promote splicing noise. We observe pervasive usage of low-fidelity splice sites, likely due to stochasticity in recruitment or binding of the spliceosome. These sites are turned over quickly and show evidence for nuclear and cytoplasmic degradation, suggesting widespread surveillance and rapid quality control of non-productive transcripts. Our findings provide insights into the propensity for error in RNA processing mechanisms and regulation of alternative splice sites across a gene.

Humans↗

PubMed2026

A latent activated olfactory stem cell state revealed by single-cell transcriptomic and epigenomic profiling.

The olfactory epithelium is one of the few regions of the nervous system that sustains neurogenesis throughout life. Its experimental accessibility makes it especially tractable for studying molecular mechanisms that drive neural regeneration in response to injury. In this study, we used single-cell sequencing to identify transcriptional and epigenetic processes involved in determining olfactory epithelial stem cell fate during injury-induced regeneration. By combining gene expression and accessible chromatin profiles of individual lineage-traced olfactory stem cells, we identified transcriptional heterogeneity among activated stem cells at a stage when cell fates are being specified. We further identified a subset of resting cells that appears poised for activation, characterized by accessible chromatin around silent genes prior to their expression in response to injury. These results provide evidence for a latent activated stem cell state in which a subset of quiescent olfactory epithelial stem cells are epigenetically primed to support injury-induced regeneration.

Animals↗

PubMed2026

Selective saccular plasticity under microgravity links peripheral transcriptomic remodeling to postflight vestibular dysfunction.

Long-duration exposure to microgravity disrupts human balance and spatial orientation, yet the molecular mechanisms underlying vestibular adaptation to spaceflight remain poorly understood. Here, we tested the hypothesis that the saccule, the primary gravity-sensing otolith organ, undergoes selective remodeling during spaceflight and contributes to transient postflight postural instability. Using a cross-species approach, we combined transcriptomic analysis of mouse otolith organs with physiological assessments in astronauts. Laser microdissection-based RNA sequencing of mouse otolith sensory epithelia after a 35-d spaceflight revealed pronounced, organ-specific transcriptomic remodeling in the saccule, whereas the utricle remained stable. Principal component and clustering analyses demonstrated that the saccular transcriptome shifted toward an utricle-like profile under microgravity, accompanied by changes in genes related to synaptic and neuronal function. Promoter motif analysis identified NFAT-associated transcriptional networks, suggesting Ca2+-dependent regulation of synaptic plasticity as a potential molecular substrate of gravity-dependent adaptation. In parallel, vestibular testing in astronauts following long-duration missions (157 to 328 d) revealed selective attenuation of saccule-mediated cervical vestibular-evoked myogenic potentials and increased postural sway immediately after return to Earth, while utricle-mediated responses and semicircular canal function were preserved. Both saccular function and postural stability recovered within approximately 10 d. Notably, early postflight postural instability was partially mitigated by noisy galvanic vestibular stimulation, consistent with stochastic resonance-mediated sensory enhancement. Together, these findings identify the saccule as a plastic gravity sensor and establish a mechanistic link between peripheral molecular remodeling and functional balance deficits after spaceflight, providing a framework for developing countermeasures to facilitate vestibular readaptation during human space exploration.

Animals↗

PubMed2026

Circadian reprogramming of inflammation and metabolism in chronic kidney disease.

BACKGROUND: Chronic kidney disease (CKD) is driven by inflammation, fibrosis, and metabolic dysfunction. While circadian rhythm dysregulation is well documented in chronic disorders, its specific impact on CKD pathogenesis remains elusive. METHODS: We performed four-hour interval time-series RNA sequencing on renal tissues from control and CKD mice. We used the JTK_CYCLE algorithm to identify rhythmic genes and categorize them as lost, acquired, or sustained in CKD; we subsequently performed focused bioinformatic analyses. RESULTS: The renal circadian profile was substantially altered; acquired rhythmicity emerged as the dominant pattern, and core clock gene expression was disrupted. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis revealed that upregulated acquired-rhythmic genes in CKD were enriched in immune-inflammatory pathways; the expression of these genes peaked at Zeitgeber time (ZT) 12-16, consistent with a higher level of renal macrophage infiltration at ZT16 than at ZT0. Conversely, genes associated with nutrient and energy metabolism pathways were downregulated but acquired rhythmicity in CKD. Dapagliflozin improved renal function and restored the circadian expression rhythms of NR1D1 and p-BMAL1. CONCLUSIONS: CKD profoundly remodels the renal circadian transcriptome, driving immune-inflammatory and metabolic pathways into maladaptive rhythmicity. Furthermore, dapagliflozin can partially restore the expression of renal core clock genes.

Animals↗

PubMed2025

Enhancing and accelerating cell type deconvolution of large-scale spatial transcriptomics slices with dual network model.

MOTIVATION: Cell type deconvolution deciphers spatial distribution of mRNA transcripts at single cell level by integrating single-cell RNA sequencing (scRNA-seq) and spatial transcriptomics data to infer mixture of cell types of spots in slices. Current algorithms are criticized for neglecting connection between scRNA-seq and spatial transcriptomics data, as well as time-consuming, hampering their application to large-scale datasets. RESULTS: In this study, we propose a joint learning nonnegative matrix factorization algorithm for fast cell type deconvolution (aka jMF2D), which integrates scRNA-seq and spatial transcriptomics data with network models. To bridge scRNA-seq and spatial transcriptomics data, jMF2D jointly learns cell type similarity network to enhance quality of signatures of cell types, thereby promoting accuracy and efficiency of deconvolution. Experiments demonstrate that jMF2D outperforms state-of-the-art baselines in terms of accuracy by saving about 90% running time on various datasets generated by different platforms. Furthermore, it can also facilitates the identification of spatial domains and bio-marker genes, providing an efficient and effective model for analyzing spatial transcriptomics data. AVAILABILITY AND IMPLEMENTATION: The software is coded using python, and is free available for academic https://github.com/xkmaxidian/jMF2D.

Algorithms↗

PubMed2026

CeLLTra: aligning cell names with gene expression via a pathway-informed transformer.

MOTIVATION: Single-cell RNA sequencing (scRNA-Seq) technology enables detailed exploration of gene expression at the individual cell level, crucial for annotating cell types and understanding cellular diversity. Traditional methods for cell type annotation often rely on marker genes and manual labeling, posing challenges due to low data quality and incomplete reference datasets. RESULTS: We developed CeLLTra, a novel contrastive learning framework that leverages a Transformer-based model integrating biological pathway information to group genes into super tokens, effectively capturing comprehensive gene expression from scRNA-Seq data. By combining this pathway-informed Transformer with a pretrained domain-specific language model, CeLLTra accurately aligns cell-type annotations with gene expression profiles. Evaluations on a large-scale human scRNA-Seq dataset showed that CeLLTra significantly outperformed state-of-the-art methods in supervised and zero-shot cell-type prediction. Additionally, CeLLTra generalized well to external datasets, improving clustering performance and enabling better characterization of cancerous cell states in tumor-infiltrating myeloid cells from non-small cell lung cancer patients. AVAILABILITY AND IMPLEMENTATION: CeLLTra is freely available on GitHub (https://github.com/WJZheng-group/CeLLTra) and Zenodo (https://doi.org/10.5281/zenodo.17666735). The datasets underlying this article are the following: GSE201333 and GSE127465. All these datasets are publicly available and can be freely accessed on the Gene Expression Omnibus repository.

Humans↗

PubMed2026

ARCADIA reveals spatially dependent transcriptional programs through integration of scRNA-seq and spatial proteomics.

MOTIVATION: Cellular states are strongly influenced by spatial context, but single-cell RNA sequencing (scRNA-seq) loses information about local tissue organization, while spatial proteomic assays capture limited marker panels that constrain transcriptomic inference. Integrating these modalities can elucidate how spatial niches shape transcriptional programs, yet existing approaches depend on either feature-level correspondence such as gene-protein linkage or cell-level barcode pairing, which is often unavailable. RESULTS: We present ARCADIA (ARchetype-based Clustering and Alignment with Dual Integrative Autoencoders), a generative framework for cross-modal integration that operates without cell barcode pairing and does not assume direct feature-to-feature correspondence. ARCADIA identifies modality-specific archetypes, that is, convex combinations of cells representing extreme phenotypic states, and aligns these anchors across modalities by minimizing the discrepancy between their cell-type composition profiles. The aligned archetypes define a shared coordinate system that anchors dual variational autoencoders (VAEs) trained with cross-modal geometric regularization, preserving archetype structure and spatial neighborhood information while enabling bidirectional translation between modalities. On semi-synthetic CITE-seq data, ARCADIA outperforms existing weak-linkage methods. Applied to independent human tonsil scRNA-seq and CODEX data, ARCADIA reconstructs known tissue architecture and reveals spatially dependent transcriptional programs linking B-cell maturation and T-cell activation or exhaustion to microenvironmental niches. AVAILABILITY AND IMPLEMENTATION: Source code is accessible at https://github.com/azizilab/ARCADIA_public. Reproducibility scripts and data are available at https://github.com/azizilab/arcadia_reproducibility.

Proteomics↗

PubMed2026

Transcriptional and phytohormonal regulation of positional ear development reveals yield strategies in maize.

Maize (Zea mays L.) is a vital global crop, contributing ∼37% of annual grain production. Enhancing yield per unit area is crucial for food security, yet research has primarily focused on single-ear traits, overlooking the regulation of double ears-a key determinant of prolificacy. While secondary ears drive yield variability under prolificacy-favoring conditions, the mechanisms governing ear formation across shoot positions remain poorly understood. Here, we performed high-resolution transcriptomic analysis of 66 samples from three ear types (primary, secondary and third) in maize inbred B73. We uncovered distinct hormonal developmental dynamics: strigolactone (SL) signaling genes, particularly SBP transcription factors, dominated in primary (I) ears, whereas ethylene-related genes (e.g., ZmEREB131, ZmACCO35) were enriched in third (III) ears. Functional validation confirmed that knockout of ZmEREB131 and ZmACCO35 accelerated development and elongated ears compared to wild-type, implicating ethylene (ETH) signaling in ear maturation arrest. Notably, SL inhibitor application synchronized primary and secondary ear development, boosting total yield by >20% without compromising primary ear performance. Our study elucidates the transcriptional networks underlying differential ear development and provides actionable strategies for yield improvement through targeted hormonal modulation. These findings advance the understanding of maize inflorescence biology and offer molecular tools for breeding high-yielding varieties.

RNA-seq↗

PubMed2026

Transcriptomic shift in ethanol and amino acid metabolic genes regulated by Med15 during alcoholic fermentation.

Organisms that thrive in extreme environments provide natural experiments in evolution, revealing the genetic regulators that orchestrate complex phenotypic change. Wine yeast (WY) are specialized strains that are adapted to survive in the wine making environment while producing high concentrations of ethanol. In addition to large genomic changes that differentiate WY from yeast used in other industries, SNP and polyglutamine tract polymorphism in the transcriptional regulator Med15 are associated with the fermentation efficiency and stress response phenotypes of WY. In this study, we investigated the transcriptional differences during wine fermentation in transgenic lab strain yeast having integrated WY MED15 alleles. Compared to the unmodified lab strain (MED15 LAB), the same strain in which the MED15 locus was replaced with a MED15 allele from yeast isolated from palm wine, the fermented sap of palm (oil, date, coconut) trees (MED15 WY23), exhibited enhanced expression of amino acid biosynthesis genes as well as stress resistance and metabolic adaptation genes. Our experimental data confirm the role of arginine in efficient fermentation and suggest that certain MED15 alleles alter the expression patterns of arginine pathway genes in some cases improving carbon flux under nitrogen stress. The global benefits conferred by natural polymorphisms in a single transcriptional regulator highlight Med15 as a target for engineering of strains devoted to various types of alcohol production.

Ethanol↗

PubMed2025

Foxi2 and Sox3 are master regulators controlling ectoderm germ layer specification.

In vertebrates, germ layer specification represents a critical transition where pluripotent cells acquire lineage-specific identities. We identify the maternal transcription factors Foxi2 and Sox3 to be pivotal master regulators of ectodermal germ layer specification in Xenopus. Ectopic co-expression of Foxi2 and Sox3 in prospective endodermal tissue induces the expression of ectodermal markers while suppressing mesendodermal markers. Transcriptomics analyses reveal that Foxi2 and Sox3 jointly and independently regulate hundreds of ectodermal target genes. During early cleavage stages, Foxi2 and Sox3 pre-bind to key cis-regulatory modules (CRMs), marking sites that later recruit Ep300 and facilitate H3K27ac deposition, thereby shaping the epigenetic landscape of the ectodermal genome. These CRMs are highly enriched within ectoderm-specific super-enhancers (SEs). Our findings highlight the pivotal role of ectodermal SE-associated CRMs in precise and robust ectodermal gene activation, establishing Foxi2 and Sox3 as central architects of ectodermal lineage specification.

Ep300↗

PubMed2025

Cell-type-specific response to silicon treatment in soybean leaves revealed by single-nucleus RNA sequencing and targeted gene editing.

Mineral nutrient uptake and deposition profoundly influence plant development, stress resilience, and productivity. Silicon (Si), though classified as a non-essential element, significantly influences a plant's physiology, particularly in fortifying defense responses and mitigating stress. While the genetic and molecular mechanisms of Si uptake and transport are well studied in monocots, particularly rice, their role in dicot species, such as soybean, remains unclear at the cellular and molecular levels. In this study, we utilized single-nucleus RNA sequencing (snRNA-seq) to dissect cellular responses to Si accumulation in soybean leaves. We identified distinct cellular populations, including a unique Si-induced or Si-associated cell cluster within vascular cells, suggesting a specialized mechanism of Si distribution. Si treatment notably induced the expression of defense-related genes, with a pronounced enrichment in vascular cells, underscoring their pivotal role in activating plant defense mechanisms. Moreover, Si modulated the expression of genes involved in phytoalexin biosynthesis, salicylic acid, and immune receptor signaling, suggesting transcriptional priming of genes involved in defense responses. Further investigation of Si transporters revealed precise expression of an Si efflux gene in epidermal cells in response to Si treatment. We also validated the role of efflux Si transporters using a Xenopus oocyte assay and CRISPR/Cas9 genome editing of composite soybean plant roots. This study provides critical insights into the biotic stress regulatory networks influenced by Si treatment in soybean leaves at the single-cell level, thus laying the foundation for enhancing stress tolerance through optimized mineral nutrient uptake.

Glycine max↗