Marchantia polymorpha, a model liverwort, provides a valuable system for investigating the evolution of plant sexual reproduction. To explore the cellular landscape of its reproductive structures, we generate a single-nucleus transcriptomic atlas of the antheridiophore, archegoniophore, and sporophyte. Using single-nucleus RNA sequencing (snRNA-seq), we capture over 30,000 high-quality nuclei and identify distinct cell populations. In the male organ, we characterize stages of spermatogenesis from early antheridium cells to mature sperm, revealing dynamic transcriptional programs including cell cycle regulation, chromatin remodelling, and calcium signalling. In the female organ, we define cell types including archegonial layers and secondary central cells. Sporophyte clusters are annotated as spores, elaters, capsule wall, foot, and seta cells, with transcriptional signatures related to structural support, stress response, and reproductive functions. Cross-species analysis indicates that capsule wall cells in liverworts are similar to tapetum cells. Notably, foot cells exhibit high expression of genes involved in sporopollenin biosynthesis and signaling pathways, serving as a central hub that mediates communication between the maternal gametophyte and the developing sporophyte. This study provides a comprehensive cellular and molecular map of M. polymorpha reproductive organs and sporophyte, establishing a framework for investigating the development and evolution of sexual reproduction in early land plants.

Cilia are vital subcellular organelles whose assembly is regulated by master transcription factors, such as Foxj1 and Rfx. However, the mechanisms of epigenetic regulation over cilia stability remain largely unclear. Here, we investigate the epigenetic control by manipulating chromatin remodeling genes in zebrafish. We demonstrate that the depletion of multiple components of the switch/sucrose non-fermentable (SWI/SNF) chromatin remodeling complex induces ciliopathy-like phenotypes in zebrafish embryos. Specifically, the loss of Actl6a, an essential component of the SWI/SNF complex, leads to cilia disassembly and cystic kidney defects, without affecting cilia motility. Our multi-omics analyses (RNA-seq, ATAC-seq, and FitCUT&RUN) consistently reveal that in Actl6a-depleted pronephros or embryos, a critical set of cilia genes, including the master regulators foxj1a and rfx2, exhibit concordant downregulation across the transcriptional level, chromatin accessibility, and SWI/SNF binding. Consistently, the depletion of foxj1a or rfx2 causes cilia assembly defects and cystic kidney formation in zebrafish. Furthermore, overexpression of either foxj1a or rfx2 mRNA substantially rescues the cystic kidney and cilia disassembly defects observed in actl6a^-/- mutant embryos. Collectively, these findings reveal that the SWI/SNF complex maintains cilia stability and kidney homeostasis by directly modulating the expression of the key ciliogenesis transcription factors foxj1a and rfx2.

Patients affected by monogenic diseases impose a substantial burden on both themselves and their families. The primary preventive measure, i.e., invasive prenatal diagnosis, carries a risk of miscarriage and cannot be performed early in pregnancy. Hence, there is a need for non-invasive prenatal testing (NIPT) for monogenic diseases. By utilizing enriched cell-free fetal DNA (cffDNA) from maternal plasma, we refine the NIPT method, which combines targeted region capture technology, haplotyping, and analysis of informative site frequency. We apply this method to 93 clinical families at genetic risk for thalassemia, encompassing various genetic variant types, to establish a workflow and evaluate its efficiency. Our approach requires only 3 ng of DNA input to generate 0.1 GB of informative target genomic data and leverages a minimum of 3% cffDNA. This method has a 98.16% success rate and 100% concordance with conventional invasive methods. Furthermore, we demonstrate the ability to analyze fetal genotypes as early as eight weeks of gestation. This study establishes an optimized NIPT method for the early detection of various thalassemia disorders during pregnancy. This technique demonstrates high accuracy and potential for clinical application in prenatal diagnosis.

The genetic basis of early-stage salt tolerance in alfalfa (Medicago sativa L.), a key factor limiting its productivity, remains poorly understand. To dissect this complex trait, we integrate genome-wide association study (GWAS) and transcriptomics (RNA-seq) from 176 accessions within a machine learning based genomic prediction framework. Analysis reveals weak genetic correlations among four salt-tolerance traits and a gradual decline in performance under increasing salt stress. GWAS identify 60 significant associated SNPs, with the highest number detected under 100 mM salt stress. Salt tolerance exhibits an additive effect from favorable haplotypes, which are most abundant in Chinese accessions. GWAS-associated genes are related to key regulators of hormone signaling and osmotic adjustment, while transcriptome analysis indicates a global repression of stress-responsive transcription factors. Integrating these multi-omics datasets allow us to identify 14 candidate genes, including MsHSD1 (seed dormancy) and MsMTATP6 (energy metabolism). Crucially, incorporating these markers into genomic prediction models improve cross-population predictive accuracy to an average of 54.4%. This study provides insights into the genetic architecture of salt tolerance in alfalfa and offers valuable markers to facilitate molecular breeding.

Hereditary cardiomyopathies and arrhythmias are major contributors to cardiovascular morbidity and mortality. The advent of next-generation sequencing (NGS) has made genetic testing more accessible, which is crucial for precise diagnosis and targeted therapeutic strategies. The aim of this study is to explore the landscape of genetic variants, the relationship between specific variants and clinical phenotypes, and the impact on clinical decision-making in China. A total of 1,536 probands (median age, 37 years; 1,025 males [66.7%]) with suspected hereditary cardiomyopathy or arrhythmia (covering 15 clinical phenotypes) are recruited from 146 hospitals across 30 provinces and cities in China. Positive results are confirmed in 390 of 1536 probands, leading to a diagnostic yield of 25.4%. Forty-two and three tenths percent (n = 169) of family members carry the same variants as positive probands. Hypertrophic cardiomyopathy (HCM) and dilated cardiomyopathy (DCM) are the predominant phenotypes, with MYBPC3 variants having the highest frequency in HCM and TTN variants in DCM. In 76.9% of the positive probands, the identified variants are helpful in clinical management, family screening and fertility. This large-scale study provides significant insights into the genetic landscape of hereditary cardiomyopathies and arrhythmias in China.

Phytochrome-interacting factors (PIFs) have been established as negative regulators of vascular patterning and xylem differentiation in the herbaceous plant Arabidopsis thaliana, however, PIFs’ regulatory role in secondary growth in woody species remains unclear. Here, we examined the expression patterns and involvement of PtoPIF3.1 and PtoPIF3.2 during stem growth and secondary xylem development in Populus tomentosa. Overexpression of either PtoPIF3.1 or PtoPIF3.2 significantly enhances both longitudinal stem growth and radial wood development. Conversely, CRISPR-generated Ptopif3.1 and Ptopif3.2 mutants exhibit reciprocal phenotypic defects. Exogenous auxin application partially restores the phenotypes of Ptopif3.1 and Ptopif3.2 mutants, and the auxin biosynthesis-deficient mutant Ptoyuc8 exhibits developmental abnormalities similar to those observed in Ptopif3 mutants. Further analysis revealed that PtoPIF3s directly bind to and activate expression of PtoYUC8 and cell expansion-related genes PtoEXPA1.1/1.2, while modulating cambial division and secondary xylem development marker genes (PtoWOX4, PtoANT, PtoCYCD3s, and PtoHB7/8) through auxin-mediated signaling. Together, our findings establish PtoPIF3.1/3.2 as key regulators that coordinate stem elongation and secondary growth in Populus, highlighting the functional divergence of PIF homologs between herbaceous and woody species.

Penetrance is a crucial indicator for accurately assessing disease risk and plays a vital role in disease research, gene therapy, and genetic counseling. However, with penetrance data dispersed across various sources, efficiently accessing and consolidating this information becomes a challenge. A comprehensive platform that integrates penetrance is urgently needed. Here, we present PenCards, a global, community-contributed public archive of variant penetrance, by first collecting penetrance data from all published literature and then using large international cohorts to specifically calculate the penetrance of autism-related variants. PenCards contains a total of 244,531 variants—including 239,244 single nucleotide variants, 4,994 insertions and deletions, and 293 copy number variants, covering approximately 300 phenotypes. We also provide a submission portal for the dynamic updating of penetrance. Additionally, to help users efficiently access genetic information, we comprehensively integrate over 150 variant- and gene-level resources. In summary, PenCards is a powerful platform designed to advance genetic research and diagnostics. PenCards is publicly available at https://genemed.tech/pencards/.

Cilia are microtubule-based organelles projecting from the cell surface with important sensory and motility functions. Ciliary defects are associated with diverse diseases collectively known as ciliopathies. However, the molecular mechanisms that govern ciliogenesis remain not fully understood. Herein, we demonstrate that ubiquitin-specific protease 21 (USP21) is indispensable for cilium formation through its deubiquitinating activity. Usp21 knockout mice exhibit ciliary defects in multiple organs, such as the kidney, liver, and trachea. Our data also reveal a constant localization of USP21 at the centrosome and basal body during ciliogenesis. Mechanistically, USP21 interacts with dihydropyrimidinase-like 2 (DYPSL2) at the centrosome and removes lysine 48-linked ubiquitination from DYPSL2. Loss of USP21 leads to the proteasomal degradation of DPYSL2 and causes a significant reduction in its centrosome abundance, ultimately resulting in ciliary defects. These findings thus identify a critical role for the USP21–DPYSL2 axis in ciliogenesis and have important implications for health and disease.

Leaf angle is a pivotal agronomic trait that significantly influences crop architecture and yield. Plant hormones, such as auxin, play a critical role in regulating leaf angle; however, the underlying molecular mechanisms remain to be fully elucidated. Here, we reveal that the auxin response factor gene, OsARF12, which is highly expressed in the leaf lamina joint, negatively regulates rice (Oryza sativa) leaf angle via affecting shoot gravitropism. Overexpression lines of OsARF12 exhibit more erect leaf angles, while the osarf12 mutants display enlarged leaf angles compared to the wild type. Further studies demonstrate that OsARF12 directly activates the expression of Loose Plant Architecture1 (LPA1) and LAZY1 by binding to their promoters. The osarf12 mutant presents impaired shoot gravitropism, a phenotype consistent with that of the lpa1 or lazy1 mutant. Collectively, we elucidate the biological functions of OsARF12, which modulates leaf angle through its impact on shoot gravitropism by regulating the expression levels of LPA1 and LAZY1. This study provides insight into the role of auxin in determining rice leaf angle, potentially holding profound effects for the optimization of crop architecture.

Modern agriculture relies heavily on resource-intensive and environmentally harmful inputs, while the increasing global population and decreasing arable land demand new strategies to improve sustainable productivity of cereal crops, particularly reducing inorganic nitrogen fertilizer use while simultaneously increasing photosynthesis and grain yield in rice. To improve rice productivity, it is essential to improve photosynthetic nitrogen assimilation and optimize the translocation of carbon and nitrogen products from source to sink tissues. In this review, we first summarize recent advances in the genetic basis for improving grain yield by enhancing photosynthetic carbon and nitrogen assimilation. We then discuss progress in modulating the source-sink relationships to achieve higher yield and improved harvest index. Finally, we explore the necessary optimizations for adapting rice to high-density planting. These advancements are driving the development of sustainable green revolution varieties through the rational design of multi-gene pyramids and artificial intelligence (AI)-driven protein engineering.

The frequency of aneuploid gamete formation increases with maternal age, yet the effects of genetic variants on meiotic chromosome segregation accuracy during aging remain poorly understood. Using the multicellular organism Caenorhabditis elegans, we investigate the impact of mutations in the conserved cohesin complex on age-associated meiotic errors. Point mutations in the head domain of the cohesin component SMC-1, which alter local hydrophobicity, cause meiotic defects that vary with age. A severe mutation causes incomplete synapsis and defective crossover formation, and a minor one causes age-related diakinesis bivalent abnormalities. Notably, while the mild mutation causes defects only in aged worms, worms with the severe mutation exhibit significantly alleviated phenotypes with age. Genetic and cytological analyses suggest that this alleviation results from a slowed meiotic progression during early prophase, which restores impaired cohesin loading. These findings reveal that cohesin variants, meiotic progression speed during early prophase, and the overall duration of meiosis collectively shape the accuracy of meiotic chromosome segregation.

Existing quantitative trait locus (QTL) mapping had low efficiency in identifying small-effect and closely linked QTL-by-environment interactions (QEIs) in RILs, especially in the era of global climate change. To address this challenge, here we integrate the compressed variance component mixed model with our GCIM to propose 3vGCIM for identifying QEIs in RILs, and extend 3vGCIM-random to 3vGCIM-fixed. 3vGCIM integrates genome-wide scanning with machine learning, significantly improving power. In the mixed full model, we consider all possible effects and control for all possible polygenic backgrounds. In simulation studies, 3vGCIM exhibits higher power (∼92.00%), higher accuracy of the estimates for QTL position (∼1.900 cM²) and effect (∼0.050), and lower false positive rate (∼0.48‰) and false negative rate (<8.10%) in three environments of 300 RILs each than ICIM (47.57%; 3.607 cM², 0.583; 2.81‰; 52.43%) and MCIM (60.30%; 5.279 cM², 0.274; 2.17‰; 39.70%). In the real data analysis of yield-related in 240 RILs, 3vGCIM mines more known genes (57∼60) and known gene-by-environment interactions (GEIs) (14∼19) and candidate GEIs (21∼23) than ICIM (27, 2, and 7), and MCIM (21, 1, and 3), especially in small-effect and linked QTLs and QEIs. This makes 3vGCIM a powerful and sensitive tool for QTL mapping and molecular QTL mapping.

Common wheat (Triticum aestivum L.) is a staple hexaploid crop with numerous wild relatives. However, domestication and modern breeding have significantly narrowed its genetic diversity, diminishing its capacity to adapt to climate change. Wild relatives of wheat serve as a vital reservoir of genetic diversity, offering traits that enhance its resistance to various biotic and abiotic stresses. Over recent decades, remarkable progress has been made in utilizing superior genes from wild relatives to bolster wheat's defenses against diseases and pests, though the exploration of genes conferring abiotic stress tolerance has lagged behind. In this review, we summarize key advancements in the utilization of wild relatives for wheat enhancement over the past century, emphasizing both theoretical and technological innovations. Furthermore, we evaluate the potential contributions of wild relatives to address production challenges posed by climate changes. We also explore strategies for isolating superior genes and developing pre-breeding germplasm to support the future development of climate-resilient wheat varieties.

Down syndrome (DS) is caused by an extra copy of chromosome 21 (Hsa21). Children with DS have an increased frequency of respiratory tract infections, impaired alveolar and vascular development, and pulmonary hypertension. How trisomy 21 causes lung diseases remains poorly understood. In this study, we use the Dp16 mouse model, which contains a segmental chromosomal duplication of the entire Hsa21 syntenic region on mouse chromosome 16, to explore the gene dosage effects on DS-related lung diseases. The Dp16 mice present impaired alveolar development and inflammatory-like pathological changes. Single-cell transcriptome (scRNA-seq) analysis highlights increased APP-related interactions among male Dp16 lung cells. Specifically, altered antigen processing and presentation with increased MHC-II signaling are found in Dp16 immune cells. Reduced angiogenesis and altered inflammatory responses of Dp16 endothelial cells are also suggested. Moreover, scRNA-seq indicates hyperplasia of Dp16 vascular smooth muscle cells, which is validated by tissue immunofluorescence assessment. Transthoracic echocardiography further shows the existence of pulmonary hypertension in young Dp16 mice. Independent scRNA-seq analysis of the female lung cells recapitulates the majority of key findings identified in male mice, confirming the reproducibility of the results. Collectively, our results provide important clues for the further development of therapeutic approaches for DS-related lung diseases.

Amyotrophic lateral sclerosis (ALS), one of the most prevalent neurodegenerative disorders, is pathologically characterized by the progressive degeneration of both upper and lower motor neurons, leading to muscle weakness, paralysis, and death within 2-4 years post-diagnosis. ALS is categorized into familial ALS (FALS) and sporadic ALS, with FALS accounting for approximately 10% of ALS cases. As a genetically heterogeneous disease, ALS exhibits diverse inheritance patterns, including autosomal dominant, autosomal recessive, and X-linked transmission, and genetic factors play pivotal roles in disease pathogenesis. To date, at least 34 disease-causing loci and 32 genes for ALS have been identified. The investigations of mutant protein products and the establishment of animal models have unraveled potential pathogenic pathways, offering insights into the mechanisms of neurodegeneration in ALS. This review focuses on ALS clinical characteristics, neuropathological features, causative loci/genes, genetic susceptibility factors, animal models, and pathogenic mechanisms, with particular attention to recent advances in genetic findings and pathogenic pathways of ALS. Elucidation of the genetic basis of ALS could provide the scientific foundation for personalized treatments to address this recalcitrant disease.

Body size control is fundamental to development and requires proper energy engagement. One of the key energy sensing factors is AMP-activated protein kinase (AMPK), which regulates glucose uptake to ensure ATP production and nutrition supply during development. Here, we identify that the mutation of xgr, a gene encoding an ATPase, results in a reduced body size in Drosophila. Xgr is primarily expressed in the epithelial cells of the Malpighian tubules and the midguts. Loss of xgr leads to the inactivation of the AMPK signaling due to an increased ATP level. Glucose reabsorption in the Malpighian tubules is significantly reduced, as the Glut1 translocation to the plasma membrane is significantly disrupted in the absence of Xgr function. Our results suggest that Xgr function in the Malpighian tubules is essential to systemic glucose supply and energy homeostasis at the organismal level, thereby impacting body size. Our findings provide a mechanistic connection between energy homeostasis and animal size control during development.

Anther is a key male reproductive organ that is essential for the plant life cycle, from the sporophyte to the gametophyte generation. To explore the isoform-level transcriptional landscape of developing anthers in maize (Zea mays L.), we analyzed Iso-Seq data from anthers collected at 10 developmental stages, together with strand-specific RNA-seq, CAGE-seq, and PAS-seq data. Of the 152,026 high-confidence full-length isoforms identified, 68.8% have not been described; these include 22,365 isoforms that originate from previously unannotated loci and 82,167 novel isoforms that originate from annotated protein-coding genes. Using our newly developed strategy to detect dynamic expression patterns of isoforms, we identified 13,899 differentially variable regions (DVRs); surprisingly, 1275 genes contain more than two DVRs, revealing highly efficient utilization of limited genic regions. We identified 7876 long non-coding RNAs (lncRNAs) from 4098 loci, most of which were preferentially expressed during cell differentiation and meiosis. We also detected 371 long-range interactions involving intergenic lncRNAs (lincRNAs); interestingly, 243 were lincRNA–gene ones, and the interacting genes were highly expressed in anthers, suggesting that many potential lncRNA regulators of key genes are required for anther development. This study provides valuable resources and fundamental information for studying the essential transcripts of key genes during anther development.

Potassium channels regulate diverse biological processes, ranging from cell proliferation to immune responses. However, the functions of potassium homeostasis and its regulatory mechanisms in adult stem cells and tumors remain poorly characterized. Here, we identify Sandman, a two-pore-domain potassium channel in Drosophila, as an essential regulator for the proliferation of intestinal stem cells and malignant tumors, while dispensable for the normal development processes. Mechanistically, loss of sandman elevates intracellular K⁺ concentration, leading to growth inhibition. This phenotype is rescued by pharmacological reduction of intracellular K⁺ levels using the K⁺ ionophore. Conversely, overexpression of sandman triggers stem cell death in most regions of the midgut, inhibits tumor growth, and induces a Notch loss-of-function phenotype in the posterior midgut. These effects are mediated predominantly via the induction of endoplasmic reticulum (ER) stress, as demonstrated by the complete rescue of phenotypes through the co-expression of Ire1 or Xbp1s. Additionally, human homologs of Sandman demonstrated similar ER stress-inducing capabilities, suggesting an evolutionarily conserved relationship between this channel and ER stress. Together, our findings identify Sandman as a shared regulatory node that governs Drosophila adult stem cell dynamics and tumorigenesis through bioelectric homeostasis, and reveal a link between the two-pore potassium channel and ER stress signaling.

In vitro maturation (IVM) of human oocytes offers cost efficiency and minimal invasiveness, serving as a valuable supplementary tool in assisted reproduction for fertility preservation, ovarian hyperstimulation syndrome prevention, and other reproductive strategies. Despite its availability for three decades, the clinical use of IVM remains limited due to efficacy and safety concerns. This study examines the DNA methylation profile of IVM oocytes collected during laparoscopic/hysteroscopic surgeries compared to in vivo matured oocytes via reduced representation bisulfite sequencing. Results indicate IVM oocytes exhibit a higher global methylation level. Differentially methylated regions (DMR) analysis reveals that the in vitro group displays more hypermethylated and fewer hypomethylated DMRs compared to the in vivo group. Additionally, the in vitro group exhibits a higher level of non-CpG methylation than the in vivo group. However, no significant correlation between methylation levels and transcriptional activity in these oocytes is found, especially for those specific imprinted genes or genes related to embryonic development. These findings shed light on the epigenetic landscape of IVM oocytes, contributing to the ongoing assessment of their clinical feasibility and safety in assisted reproduction.

While methodology for determining the mode of evolution in coding sequences has been well established, evaluation of adaptation events in emerging types of phenotype data needs further development. Here we propose an analysis framework (expression variance decomposition, EVaDe) for comparative single-cell expression data based on phenotypic evolution theory. After decomposing the gene expression variance into separate components, we use two strategies to identify genes exhibiting large between-taxon expression divergence and small within-cell-type expression noise in certain cell types, attributing this pattern to putative adaptive evolution. In a dataset of primate prefrontal cortex, we find that such human-specific key genes enrich with neurodevelopment-related functions, while most other genes exhibit neutral evolution patterns. Specific neuron types are found to harbor more of these key genes than other cell types, thus likely to have experienced more extensive adaptation. Reassuringly, at molecular sequence level, the key genes are significantly associated with the rapidly evolving conserved non-coding elements. An additional case analysis comparing the naked mole-rat (NMR) with the mouse suggests that innate-immunity-related genes and cell types have undergone putative expression adaptation in NMR. Overall, the EVaDe framework may effectively probe adaptive evolution mode in single-cell expression data.

Understanding how species diverge and adapt is fundamental to unraveling biodiversity. While environmental impacts on species evolution are well-documented, the roles of intrinsic life-history traits remain underexplored. The Qinghai-Tibet Plateau, with its harsh conditions and unique biodiversity, offers a natural laboratory for such investigations. Here, we examined two sympatric small mammals—the solitary, low-dispersal plateau zokor (Eospalax baileyi) and the social, high-dispersal plateau pika (Ochotona curzoniae)—to elucidate how life-history traits shape population structures and adaptive strategies. Through whole-genome sequencing and cardiac-blood phenotype analyses, we reveal striking differences in their evolutionary trajectories. Despite enduring similar environmental pressures, plateau zokor populations exhibit pronounced genetic subdivisions, high inbreeding, and distinct local adaptations. In contrast, plateau pika populations display genetic panmixia, widespread diversity, and adaptive uniformity. Demographic inference highlights plateau zokors experienced severe population bottlenecks and restricted gene flow during glacial periods, underscoring the impact of dispersal capacity on evolutionary outcomes. Our findings demonstrate that intrinsic biological traits, particularly dispersal ability, fundamentally influence genetic architecture, population connectivity, and local adaptation. This study not only provides empirical evidence of how life-history traits shape evolutionary dynamics but also offers a framework for integrating intrinsic and extrinsic factors in understanding biodiversity formation.

The occurrence of severe thalassemia, an inherited blood disorder that is either blood-transfusion-dependent or fatal, can be mitigated through carrier screening. Here, we aim to evaluate the effectiveness and outcomes of pre-conceptional and early pregnancy screening initiatives for severe thalassemia prevention in a diverse population of 28,043 women. Using next-generation sequencing (NGS), we identify 4,226 (15.07%) thalassemia carriers across 29 ethnic groups and categorize them into high- (0.75%), low- (25.86%), and unknown-risk (69.19%) groups based on their spouses’ screening results. Post-screening follow-up reveals 59 fetuses with severe thalassemia exclusively in high-risk couples, underscoring the efficacy of risk classification. Among 25,053 live births over 6 months of age, two severe thalassemia infants were born to unknown-risk couples, which was attributed to incomplete screening and late NGS-based testing for a rare variant. Notably, 64 rare variants are identified in 287 individuals, highlighting the genetic heterogeneity of thalassemia. We also observe that migrant flow significantly impacts carrier rates, with 93.90% of migrants to Chenzhou originating from high-prevalence regions in southern China. Our study demonstrates that NGS-based screening during pre-conception and early pregnancy is effective for severe thalassemia prevention, emphasizing the need for continuous screening efforts in areas with high and underestimated prevalence.

Cell competition is an evolutionarily ancient mechanism that functions to remove unfit or dangerous clonal cells in a multicellular community. A classical model is the removal of polarity-deficient clones, such as the precancerous scribble (scrib) mutant clones, in Drosophila imaginal discs. The activation of Ras, Yki, or Notch signaling robustly reverses the scrib mutant clonal fate from elimination to tumorous growth. Whether these signals converge to adopt a common mechanism to overcome the elimination pressure posed by cell competition remains unclear. Using single-cell transcriptomics, we find that a critical converging point downstream of Ras, Yki, and Notch signals is the upregulation of Upd2, an IL-6 family cytokine. Overexpression of Upd2 is sufficient to rescue the scrib mutant clones from elimination. Depletion of Upd2 blocks the growth of the scrib mutant clones with active Ras, Yki, and Notch signals. Moreover, Upd2 overexpression promotes robust intestinal stem cell (ISC) proliferation, while Upd2 is intrinsically required in ISCs for the growth of the adult intestine. Together, these results identify Upd2 as a crucial cell fitness factor that sustains tissue growth but can potentiate tumorigenesis when deregulated.

Translation is a crucial step in gene expression. Over the past decade, the development and application of Ribosome profiling (Ribo-seq) have significantly advanced our understanding of translational regulation in vivo. However, the analysis and visualization of Ribo-seq data remain challenging. Despite the availability of various analytical pipelines, improvements in comprehensiveness, accuracy, and user-friendliness are still necessary. In this study, we develop RiboParser/RiboShiny, a robust framework for analyzing and visualizing Ribo-seq data. Building on published methods, we optimize ribosome structure-based and start/stop-based models to improve the accuracy and stability of P-site detection, even in species with a high proportion of leaderless transcripts. Leveraging these improvements, RiboParser offers comprehensive analyses, including quality control, gene-level analysis, codon-level analysis, and the analysis of Ribo-seq variants. Meanwhile, RiboShiny provides a user-friendly and adaptable platform for data visualization, facilitating deeper insights into the translational landscape. Furthermore, the integration of standardized genome annotation renders our platform universally applicable to various organisms with sequenced genomes. This framework has the potential to significantly improve the precision and efficiency of Ribo-seq data interpretation, thereby deepening our understanding of translational regulation.

Hearing and balance disorders are significant health issues primarily caused by developmental defects or the irreversible loss of sensory hair cells (HCs). Identifying the underlying genes involved in the morphogenesis and development of HCs is crucial. Our current study highlights rhpn2, a member of rho-binding proteins, as essential for vestibular HC development. The rhpn2 gene is highly expressed in the crista and macula HCs. Loss of rhpn2 function in zebrafish reduces the otic vesicle area and vestibular HC number, accompanied by vestibular dysfunction. Shorter stereocilia and compromised mechanotransduction channel function are found in the crista HCs of rhpn2 mutants. Transcriptome RNA sequencing analysis predicts the potential interaction of rhpn2 with rhoab. Furthermore, co-immunoprecipitation confirms that Rhpn2 directly binds to RhoA, validating the interaction of the two proteins. rhpn2 knockout leads to a decreased expression of rock2b, a canonical RhoA signaling pathway gene. Treatment with the RhoA activator or exogenous rock2b mRNA injection mitigates crista HC stereocilia defects in rhpn2 mutants. This study uncovers the role of rhpn2 in vestibular HC development and stereocilia formation via mediating the RhoA signaling pathway, providing a target for the treatment of balance disorders.

α-Zeins, the major maize endosperm storage proteins, are transcriptionally regulated by Opaque 2 (O2) and PROLAMIN-BOX BINDING FACTOR1 (PBF1), with Opaque 11 (O11) functioning upstream of them. However, whether O11 directly binds to α-zein genes and its regulatory interactions with O2 and PBF1 remain unclear. Using the small-kernel mutant sw1, which exhibits decreased 19-kDa and increased 22-kDa α-zein, we positionally cloned O11 and found it directly binds to G-box/E-box motifs. O11 activates 19-kDa α-zein transcription, stronger than PBF1 but weaker than O2. Notably, PBF1 competitively binds to overlapping E-box/P-box motif, and represses O11-mediated transactivation. Although O11 does not physically interact with O2, it participates in the O2-centered hierarchical network to enhance α-zein expression. sw1 o2 and sw1 pbf1 double mutants exhibit smaller, more opaque kernels with further reduced 19-kDa and 22-kDa α-zeins compared to the single mutants, suggesting distinct regulatory effects of these transcription factors on 19-kDa and 22-kDa α-zein genes. Promoter motif analysis suggests that O11, PBF1, and O2 directly regulate 19-kDa α-zein genes, while O11 indirectly controls 22-kDa α-zein genes via O2 and PBF1 modulation. These findings identify the unique and coordinated roles of O11, O2, and PBF1 in regulating α-zein genes and kernel development.

Mediator Complex Subunit 16 (MED16, MIM: 604062) is a member of the Mediator complex, which controls many aspects of transcriptional activity in all eukaryotes. Here, we report two individuals from a non-consanguineous family with biallelic variants in MED16 identified by exome sequencing. The affected individuals present with global developmental delay, intellectual disability, and dysmorphisms. To assess the pathogenicity of the variants, functional studies are performed in Drosophila and patient-derived cells. The fly ortholog med16 is expressed in neurons and some glia of the developing central nervous system (CNS). Loss of med16 leads to a reduction in eclosion and lifespan, as well as impaired synaptic transmission. In neurons differentiated from the patient-derived induced pluripotent stem cells (iPSCs), the neurite outgrowth is impaired and rescued by expression of exogenous MED16. The patient-associated variants behave as loss-of-function (LoF) alleles in flies and iPSCs. Additionally, the transcription of genes related to neuronal maturation and function is preferentially altered in patient cells relative to differentiated H9 controls. In summary, our findings support that MED16 is important for appropriate development and function, and that biallelic MED16 variants cause a neurodevelopmental disease.

Nitric oxide (NO) is a key vasodilator that regulates vascular pressure and blood flow. Tibetans have developed a “blunted” mechanism for regulating NO levels at high altitude, with GTP cyclohydrolase 1 (GCH1) identified as a key candidate gene. Here, we present comprehensive genetic and functional analyses of GCH1, which exhibits strong Darwinian positive selection in Tibetans. We show that Tibetan-enriched GCH1 variants down-regulate its expression in the blood of Tibetans. Based on this observation, we generate the heterozygous Gch1 knockout (Gch1^+/–) mouse model to simulate its downregulation in Tibetans. We find that under prolonged hypoxia, the Gch1^+/– mice have relatively higher blood NO and blood oxygen saturation levels compared with the wild-type (WT) controls, providing better oxygen supplies to the cardiovascular and pulmonary systems. Markedly, hypoxia-induced cardiac hypertrophy and pulmonary remodeling are significantly attenuated in the Gch1^+/– mice compared with the WT controls, likely due to the adaptive changes in molecular regulations related to metabolism, inflammation, circadian rhythm, extracellular matrix, and oxidative stress. This study sheds light on the role of GCH1 in regulating blood NO, contributing to the physiological adaptation of the cardiovascular and pulmonary systems in Tibetans at high altitude.

Astrocyte maturation is crucial for brain function, yet the mechanisms regulating this process remain poorly understood. In this study, we identify the bHLH transcription factors Olig1 and Olig2 as essential coordinators of cortical astrocyte maturation. We demonstrate that Olig1 and Olig2 work synergistically to regulate cortical astrocyte maturation by modulating Bmp7 expression. Genetic ablation of both Olig1 and Olig2 results in defective astrocyte morphology, including reduced process complexity and an immature gene expression profile. Single-cell RNA sequencing reveals a shift towards a less mature astrocyte state, marked by elevated levels of HOPX and GFAP, resembling human astrocytes. Mechanistically, Olig1 and Olig2 bind directly to the Bmp7 enhancer, repressing its expression to promote astrocyte maturation. Overexpression of Bmp7 in vivo replicates the astrocyte defects seen in Olig1/2 double mutants, confirming the critical role of BMP7 signaling in this process. These findings provide insights into the transcriptional and signaling pathways regulating astrocyte development and highlight Olig1 and Olig2 as key regulators of cortical astrocyte maturation, with potential implications for understanding glial dysfunction in neurological diseases.

Hearing relies on the structural and functional integrity of cochlear hair cells, particularly their apical F-actin-filled stereocilia. Phospholipid scramblases are important for maintaining membrane asymmetry, but their roles in the stereocilia and auditory functions are not fully understood. Here, we identify Plscr5 as a downstream target of the transcription factor POU4F3 essential for hair cell function, whose mutation causes human DFNA15 deafness. Plscr5 knockout mice exhibit progressive hearing loss due to stereocilia degeneration and hair cell loss. Functional analyses reveal that PLSCR5 contributes to phosphatidylserine externalization in hair cell apical membranes, particularly in inner hair cells, and is important for outer hair cell and stereocilia maintenance. Our findings highlight PLSCR5 as an important downstream effector of POU4F3 and regulator of PS externalization and membrane dynamics required for auditory functions.

Although the spatial characteristics within the tumor microenvironment (TME) of lung adenocarcinoma (LUAD) have been identified, the mechanisms by which these factors promote LUAD progression and immune evasion remain unclear. Using spatial transcriptomics (ST) and single-cell RNA-sequencing (scRNA-seq) data from multi-regional LUAD biopsies consisting of tumor core, tumor edge, and normal area, we sought to delineate the spatial heterogeneity and driving factors of cell colocalization. Two cancer cell sub-clusters (Cancer_c1 and Cancer_c2), associated with LUAD initiation and metastasis, respectively, exhibit distinct spatial distributions and immune cell colocalizations. In particular, Cancer_c1, enriched within the tumor core, could directly interact with B cells or indirectly recruit B cells through macrophages. Conversely, Cancer_c2 enriched within the tumor edge exhibits colocalization with CD8⁺ T cells. Collectively, our work elucidates the spatial distribution of cancer cell subtypes and their interaction with immune cells in the core and edge of LUAD, providing insights for developing therapeutic strategies for cancer intervention.

Sex-specific neurons play pivotal roles in regulating sexually dimorphic behaviors. In insects, the sex determination gene doublesex (dsx) establishes major sexual dimorphism of the nervous system, in which male-specific dsx^M promotes neuronal development, while female-specific dsx^F inhibits neuronal development by promoting neuronal apoptosis. In this study, we find that dsx regulates the number of dsx-expressing central neurons in Drosophila in cell-specific manners. Although dsx^M overall promotes an increase in the number of dsx neurons, it inhibits the emergence of specific pC1 neurons. dsx^F reduces the number of different pC1/pC2 subtypes, but promotes the formation of pC1d. We also find that dsx^M and dsx^F barely affect the number of some pC2 neurons. Changes in the number of pC1/pC2 neuron numbers alter their roles in regulating different behaviors, including courtship, aggression, and locomotion. Our results illustrate the multifaceted functions of dsx in sexually dimorphic neuronal development and behaviors.

The impact of mother-infant microbiota on neurodevelopment is an area of interest, but longitudinal studies are scarce. Using a cohort of 520 families from the Jiangsu birth cohort in China, we reveal that the maternal gut microbiota during early pregnancy play a substantial role, accounting for 3.34% of the variance in offspring neurodevelopmental scores. This contribution is notably higher than the 1.24% attributed to the infants’ own microbiota at 1 year of age, underscoring the significant influence of maternal gut health on early child development. Remarkably, an elevation in maternal Bifidobacterium pseudocatenulatum is linked to decreased cognitive scores, whereas an enrichment of Bifidobacterium longum at 1 year of age is associated with higher cognitive scores. Furthermore, we find that maternal B. pseudocatenulatum is linked to the heterolactic fermentation metabolic pathway, while infant B. longum is associated with the Bifidobacterium shunt pathway. In summary, our analysis implies that maternal and infant gut microbiota play a distinct role in neurodevelopment, suggesting potential strategies for improving neurodevelopmental outcomes during early pregnancy or infant development by targeting gut microbiota composition.

Agricultural pests cause enormous losses in annual agricultural production. Understanding the evolutionary responses and adaptive capacity of agricultural pests under climate change is crucial for establishing sustainable and environmentally friendly agricultural pest management. In this study, we integrate climate modeling and landscape genomics to investigate the distributional dynamics of the cotton bollworm (Helicoverpa armigera) in the adaptation to local environments and resilience to future climate change. Notably, the predicted inhabitable areas with higher suitability for the cotton bollworm could be eight times larger in the coming decades. Climate change is one of the factors driving the dynamics of distribution and population differentiation of the cotton bollworm. Approximately 19,000 years ago, the cotton bollworm expanded from its ancestral African population, followed by gradual occupations of the European, Asian, Oceanian, and American continents. Furthermore, we identify seven subpopulations with high dispersal and adaptability which may have an increased risk of invasion potential. Additionally, a large number of candidate genes and SNPs linked to climatic adaptation were mapped. These findings could inform sustainable pest management strategies in the face of climate change, aiding future pest forecasting and management planning.

The liver performs several vital functions such as metabolism, toxin removal, and glucose storage through the coordination of various cell types. With the recent breakthrough of the single-cell/single-nucleus RNA-seq (sc/snRNA-seq) techniques, there is a great opportunity to establish a reference cell map of the liver at single-cell resolution with transcriptome-wise features. In this study, we build a unified liver cell atlas uniLIVER (http://lifeome.net/database/uniliver) by integrative analysis of a large-scale sc/snRNA-seq data collection of normal human liver with 331,125 cells and 79 samples from 6 datasets. Moreover, we introduce LiverCT, a novel machine learning based method for mapping any query dataset to the liver reference map by introducing the definition of “variant” cellular states analogy to the sequence variants in genomic analysis. Applying LiverCT on liver cancer datasets, we find that the “deviated” states of T cells are highly correlated with the stress pathway activities in hepatocellular carcinoma, and the enrichments of tumor cells with the hepatocyte-cholangiocyte “intermediate” states significantly indicate poor prognosis. Besides, we find that the tumor cells of different patients have different zonation tendencies and this zonation tendency is also significantly associated with the prognosis. This reference atlas mapping framework can also be extended to any other tissues.

Ferroptosis, a type of programmed cell death, represents a distinct paradigm in cell biology. It is characterized by the iron-dependent accumulation of reactive oxygen species, which induce lipid peroxidation (LPO), and is orchestrated by the interplay between iron, lipid peroxides, and glutathione. In this review, we emphasize the frequently overlooked role of iron in LPO beyond the classical iron-driven Fenton reaction in several crucial processes that regulate cellular iron homeostasis, including iron intake and export as well as ferritinophagy, and the emerging roles of endoplasmic reticulum-resident flavoprotein oxidoreductases, especially P450 oxidoreductases, in modulating LPO. We summarize how various types of fatty acids (FAs), including saturated, monounsaturated, and polyunsaturated FAs, differentially influence ferroptosis when incorporated into phospholipids. Furthermore, we highlight the therapeutic potential of targeting LPO to mitigate ferroptosis and discuss the regulatory mechanisms of endogenous lipophilic radical-trapping antioxidants that confer resistance to ferroptosis, shedding light on therapeutic avenues for ferroptosis-associated diseases.

The crop yields achieved through traditional plant breeding techniques appear to be nearing a plateau. Therefore, it is essential to accelerate advancements in photosynthesis, the fundamental process by which plants convert light energy into chemical energy, to further enhance crop yields. Research focused on improving photosynthesis holds significant promise for increasing sustainable agricultural productivity and addressing challenges related to global food security. This review examines the latest advancements and strategies aimed at boosting crop yields by enhancing photosynthetic efficiency. There has been a linear increase in yield over the years in historically released germplasm selected through traditional breeding methods, and this increase is accompanied by improved photosynthesis. We explore various aspects of the light reactions designed to enhance crop yield, including light harvest efficiency through smart canopy systems, expanding the absorbed light spectrum to include far-red light, optimizing non-photochemical quenching, and accelerating electron transport flux. At the same time, we investigate carbon reactions that can enhance crop yield, such as manipulating Rubisco activity, improving the Calvin-Benson-Bassham (CBB) cycle, introducing CO₂ concentrating mechanisms (CCMs) in C₃ plants, and optimizing carbon allocation. These strategies could significantly impact crop yield enhancement and help bridge the yield gap.