Primary metabolites and their derivatives often serve as intracellular signals. Inositol pyrophosphates are central regulators of phosphate signaling, but their roles in legume nodulation remain poorly understood. Here, we identify two conserved Vip1 Homolog/Diphosphoinositol Pentakisphosphate Kinase genes, MtVIH1 and MtVIH2, in Medicago truncatula. Biochemical analyses show that the kinase domains of both MtVIH1 and MtVIH2 retain PP-InsP kinase activity. However, transcriptomic and expression analyses reveal regulatory divergence between the duplicated genes, with MtVIH2 being preferentially induced during nodulation and co-expressed with the phosphate starvation marker Mt4. Silencing MtVIH2 reduces nodule formation, nitrogenase activity, and mature nodule marker expression, and alters extractable inorganic Pi accumulation in nodules. Consistently, CRISPR/Cas9-mediated editing of MtVIH2 reproduces these defects, whereas Mtvih1-cas9 shows much weaker effects and Mtvih1/2-cas9 edited roots display phenotypes comparable to Mtvih2-cas9. These results demonstrate that regulatory divergence between duplicated VIH genes is associated with a predominant role of MtVIH2 in nodule development. Promoter analysis and luciferase assays reveal that a P1BS element contributes to MtPHR1-mediated activation of the MtVIH2 promoter. Together, these findings reveal regulatory divergence of duplicated VIH genes and suggest that conserved phosphate-responsive mechanisms contribute to nodule development and nitrogen fixation in M. truncatula.
Soil inorganic nitrogen (N) availability is a critical determinant of symbiotic nitrogen fixation efficiency, making it essential for legumes to respond appropriately and effectively to N fluctuations. Here, we identify a pair of high N response factors GmNIGT2a/2b (NITRATE-INDUCIBLE GARP-TYPE TRANSCRIPTIONAL REPRESSOR). GmNIGT2a/2b are activated by GmNLP4a/b (NIN-like proteins) under high N. The nodules of gmnigt2a/2b double mutants exhibit exacerbated reduction in nitrogenase activity and accelerated senescence in response to high N. Integration of RNA-seq and DAP-seq analyses reveals that GmNIGT2a/2b negatively regulate a suite of core N-induced genes, including NAC, WRKY, and bZIP transcription factors as well as trehalose metabolism genes. GmNIGT2b binds to the promoters of SNAP3 and NAC039 and represses their expression, thereby delaying nodule senescence. Our results suggest that GmNIGT2a/2b-mediated transcriptional regulation prevents excessive nodule senescence in response to high N, highlighting the complexity of transcriptional reprogramming for environmental adaptation in nodules.
The evolutionary origins of adaptive immune diversification remain a central question in immunology. Using zebrafish as an early vertebrate model, we systematically dissect the distinct diversification strategies of ancient IgM and IgZ antibody repertoires. While both isotypes share a common V gene pool, they exhibit lineage-specific V/J usage biases during independent V(D)J recombination. Heavy-chain rearrangement employs the recombination-activating gene-non-homologous end joining (RAG-NHEJ) pathway, with IgM demonstrating greater junctional diversity than IgZ. Antigen-driven somatic hypermutation (SHM) primarily targets IgM via activation-induced cytidine deaminase (AID)-primed base excision repair/mismatch repair within primitive germinal center-like clusters. However, unbiased targeting across complementarity determining and framework regions, together with constrained CXCR5-CXCL13 signaling, limits mutation frequency and affinity maturation. Notably, we identify an AID-independent SHM pathway mediated by APOBEC2a that specifically targets TCG/CGT motifs. Furthermore, light-chain V-J recombination is uniquely processed via microhomology-mediated end joining, restricting CDR3 diversity compared with heavy-chain. Conversely, IgZ+ B cells are biased toward plasma cell differentiation, exhibit loosely organized distribution, and undergo minimal antigen-driven SHM, aligning with rapid mucosal defense. Our findings reveal both conserved and distinct diversification mechanisms in teleosts, illuminating layered evolutionary strategies balancing receptor diversity and self-tolerance in early vertebrates.
Alternative polyadenylation (APA) generates transcript diversity by producing mRNA isoforms with distinct 3' untranslated regions (3' UTRs) or coding sequences. Existing single-cell RNA sequencing (scRNA-seq) methods for APA analysis primarily rely on Read2 data, which lacks precise cleavage site (CS) information and limits accurate polyadenylation site (PAS) identification. Here, we present single-cell PolyAdenylation ISOform quantification (scPAISO), a computational pipeline that leverages the often-discarded Read1 from 3' tag-based scRNA-seq to enable de novo PAS identification and PAS isoform quantification. Unlike existing approaches, scPAISO directly captures mRNA 3' end cleavage sites, resulting in stronger AAUAAA motif enrichment, sharper PAS peaks, and improved spatial resolution for resolving closely spaced PASs. Across multiple datasets and biological systems, scPAISO robustly identified PASs and quantified APA dynamics, revealing stage-specific 3' UTR lengthening during hematopoietic differentiation, widespread 3' UTR remodeling in systemic sclerosis, and tissue-specific polyadenylation preferences associated with distinct RNA-binding protein programs in mice. scPAISO provides an accurate and scalable framework for single-cell APA analysis, enabling high-resolution characterization of post-transcriptional regulation and transcriptome diversity in development, physiology, and disease.
The integration of environmental and developmental cues into coherent physiological responses is fundamental to plant survival. Reactive oxygen, nitrogen, and sulfur species (ROS/RNS/RSS) are now recognized as essential signaling molecules, not merely cytotoxic byproducts. Their specificity is largely achieved through reversible, site-specific cysteine oxidative post-translational modifications (Cys-OxiPTMs), which constitute a dynamic and sophisticated "redox code". This review provides a systematic synthesis of the current landscape of Cys-OxiPTMs in plants, bridging chemistry, hormone biology, agronomy, detection, and engineering. The chemical and enzymatic basis of major Cys-OxiPTMs is detailed, along with a discussion of how their spatiotemporal interplay orchestrates signaling specificity. A critical examination is then presented on how these modifications decode and integrate plant hormone signaling networks to regulate key agronomic traits. Cutting-edge proteomic technologies that have revolutionized the identification of redox-sensitive cysteines are also evaluated. Finally, forward-looking strategies to "write" the redox code are explored. By moving the field from descriptive cataloging to predictive "redox breeding," this review establishes a foundational framework for manipulating Cys-OxiPTMs to develop climate-resilient, high-yielding crops for sustainable agriculture.
The maintenance of homeostasis in hematopoietic stem and progenitor cells (HSPCs) is essential for the proper development of the entire hematopoietic system. However, the mechanisms underlying this regulatory equilibrium remain elusive. Here, we report that Prdm15 deficiency in HSPCs induces the accumulation of immature hematopoietic stem cells in mice. A series of transplantation assays shows that these cells display impaired reconstitution capacity and competitive fitness, which are associated with abnormal differentiation trajectories and transcriptional alterations identified by single-cell RNA sequencing. Mechanistically, integrated multi-omics analyses including ATAC-seq and CUT&Tag sequencing of HSPCs indicate that Prdm15 deficiency induces significant transcriptional and epigenetic alterations, particularly affecting the methyltransferase KMT2C and altering H3K4me1 and H3K27ac modifications at the promoters of hematopoietic developmental genes. Collectively, our findings establish PRDM15 as a critical epigenetic regulator of HSPCs, offering valuable insights into the molecular mechanisms underlying hematopoietic homeostasis.
Widespread potassium (K) deficiency in paddy soils, coupled with the low potassium use efficiency (KUE) of rice, has driven research on genetically improving KUE for sustainable rice production. Breeding high-KUE rice cultivars requires thorough understanding of root K+ uptake molecular mechanisms mediated by specific K+ channels and transporters. Here, we characterize the Shaker-type K+ channel OsKAT1 in rice. Disruption of OsKAT1 impairs root K+ uptake, resulting in reduced K+ accumulation and severe growth retardation under low-K+ stress. Conversely, overexpression of OsKAT1 enhances root K+ acquisition and promotes rice growth. Notably, OsKAT1-overexpressing lines exhibit increased culm diameter and improved bending resistance, thereby enhancing lodging tolerance. OsKAT1 overexpression also significantly increases grain size and weight under both K+-sufficient and low-K+ conditions. Natural variation at the OsKAT1 locus correlates with differential gene expression among haplotypes, with Hap 2 and Hap 3 conferring superior tolerance to low-K+ stress. Additionally, our results suggest that the expression pattern and physiological function of OsKAT1 may be cultivar-dependent. Collectively, these findings establish OsKAT1 as a key integrator of low-K+ adaptation, lodging resistance, and yield enhancement in rice, offering a promising genetic target for breeding rice varieties with improved KUE and yield potential.
The structural integrity of the sperm flagellum is essential for male fertility, and its impairment is associated with reduced sperm motility. The sperm annulus is a septin-based fibrous ring that demarcates the midpiece and the principal piece. Notably, defects in sperm annulus formation frequently co-occur with abnormalities in flagellar structure; however, the underlying molecular mechanisms remain poorly understood. Herein, we identify an evolutionarily conserved leucine-rich repeat-containing protein, LRRC71, and show that its deficiency results in spermatozoa with a shortened mitochondrial sheath and a defective annulus, ultimately leading to male infertility. Further analysis reveals that LRRC71 deficiency leads to reduced sperm motility and decreased ATP levels following capacitation, effects that are potentially driven by a metabolic shift from oxidative phosphorylation to glycolysis. In addition, the protein levels of SEPT4, SEPT5, and SEPT7 are significantly reduced in Lrrc71-null spermatids. Mechanistically, LRRC71 directly binds SEPT4 via its N-terminal domain, thereby stabilizing the sperm annulus. Furthermore, the exogenous expression of SEPT4 rescues both motility and annulus defects in Lrrc71-null spermatozoa, confirming this functional hierarchy. Collectively, our findings demonstrate that LRRC71 serves as a central hub stabilizing sperm annulus integrity, providing insights into the pathogenic mechanisms underlying infertility associated with downregulation of LRRC71 in humans.
Breeding sheep with superior growth performance and wool quality is essential for the sustainability of the fine-wool sheep industry. In this study, we perform low-coverage whole-genome sequencing (lcWGS) on 3842 individuals from 5 sheep breeds (4 fine-wool and 1 semi-fine wool) and generate a large genomic dataset. By comparing these breeds with coarse-wool sheep, we characterize the genomic landscape and selection signatures of fine-wool sheep. We identify several known functional genes associated with hair follicle development and skin morphology, including EGFR, KRT74, EDAR, EREG, and GLI2. Furthermore, GWAS of 19 traits identifies 156 candidate genes significantly associated with growth and wool characteristics, including LCORL for body size, EGFR for clean wool yield, and PRDM1 for fiber diameter. Notably, EGFR is detected in both GWAS and selection signature analyses, indicating its important role in phenotype formation and historical selection. Overall, our findings reveal the genetic basis of growth and wool traits in fine-wool and semi-fine wool sheep, highlight EGFR, LCORL, and PRDM1 as candidate genes, and provide valuable genomic resources and candidate markers for future functional validation and molecular breeding.
Neurogenetic disorders have been recognized clinically for decades, and advances in clinical and genetic studies have identified more than 1700 monogenic causes of neurological diseases. Various types of mutations, including missense, truncating, and repeat expansions, have been reported in patients with neurogenetic disorders. It is now recognized that incomplete penetrance is common, with some individuals carrying disease-causing mutations remaining clinically unaffected. However, there is currently no comprehensive conceptual framework to categorize or explain these observations. Here, we review and integrate decades of evidence on incomplete penetrance in neurogenetic disorders to clarify its biological and mechanistic bases. Accordingly, four major themes are identified, encompassing genetic modifiers, epigenetic modifications, mosaicism, and environmental factors. These factors may act independently or interactively to influence pathogenic burden and functional network balance, ultimately determining whether a pathogenic mutation manifests clinically. Based on these insights, we highlight emerging perspectives and propose future research to fill gaps in our understanding. A deeper understanding of incomplete penetrance will be essential for generating genetic insights to support more effective genetic counseling, therapeutic interventions, and disease prevention in neurogenetic disorders.
Cancer remains the leading cause of death worldwide, presenting substantial challenges to precision medicine due to its complex heterogeneity. Radiogenomics, as a method combining quantitative radiologic data with genomic information, provides a robust analysis framework to assess tumor heterogeneity and cancer progression. Here, we summarize the application of radiogenomics in two key fusion methods: feature-level and decision-level fusion. Feature-level fusion combines multimodal data into a rich feature set to improve the predictive power of models, while decision-level fusion integrates decision results from multiple independent models to improve robustness and reliability. Furthermore, we explore the integration of radiomics with various omics technologies, including transcriptomics, metabolomics, and proteomics. This integration enables a deeper understanding of the dynamic tumor microenvironment, metabolic dysregulation, and cancer progression mechanisms. Finally, we provide a detailed overview of publicly available datasets relevant to radiogenomics research, such as The Cancer Imaging Archive, cBioPortal, UK Biobank, and Human Connectome Project; and further describe multiple types of omics data and sample characteristics for each resource for the benefit to readers. In summary, this review charts a path beyond radiogenomics by advancing radiomics and multi-omics horizons to transform precision medicine in cancer.
