Gene最新文献

{"title":"Innovative minicircle DNA vector encoding pri-miR-375 silences E6 and E7 oncoproteins in HPV16-positive CaSki cells","authors":"D. Pereira ,&nbsp;A.M. Almeida ,&nbsp;J.A. Queiroz ,&nbsp;F. Sousa ,&nbsp;N. Alves ,&nbsp;J.F.A. Valente ,&nbsp;A. Sousa","doi":"10.1016/j.gene.2025.149964","DOIUrl":"10.1016/j.gene.2025.149964","url":null,"abstract":"<div><h3>Background</h3><div>The infection by Human Papillomaviruses (HPV) has long been established as one of the main causes of cervical cancer, with HPV16/HPV18 high-risk types expressing E6/E7 oncoproteins that inhibit p53/pRB tumor suppressor proteins. Therefore, this work focuses on gene therapy, using the innovative minicircle DNA (mcDNA) vector to protect and express the pri-miR-375 in the cancer cell nucleus, ultimately originating the microRNA-375 (miR-375) in the cytoplasm. This miR-375, initially downregulated in cervical cancer cells, can silence HPV E6/E7 transcripts, thereby negatively regulating the expression of these oncoproteins.</div></div><div><h3>Methods</h3><div>The mcDNA-pri-miR-375 vector was successfully constructed, biosynthesized in the host cell, extracted, and purified, followed by several <em>in vitro</em> transfection studies in CaSKi cells (HPV16-infected cervical cancer model) to evaluate the mcDNA-pri-miR-375 effect.</div></div><div><h3>Results</h3><div>FITC-stained-mcDNA-pri-miR-375 was present in cancer cell nucleus, confirmed by confocal microscopy. RT-PCR analysis showed a more intense band of miR-375 transcripts, and RT-PCR/ RT-qPCR confirmed that E6/ E7 transcript levels were nearly 80 % diminished 24 h after CaSki cells transfection. Also, western-blot showed a decreased band intensity for E6/ E7 proteins on transfected cells. Proliferation and cell invasion studies demonstrated growth and migration arrest for CaSki cells throughout 72 h. Cell viability study of these cells also revealed a gradual decrease for the same period, while the NHDF cell viability was not affected, indicating specificity towards CaSki. The consequent effect of silencing the E6/ E7 transcripts was also observed through an increase in p53 protein levels (determined by western blot and ELISA) and caspase-3 activity, after 48 h of CaSki cell transfection.</div></div><div><h3>Conclusions</h3><div>These results suggest that mcDNA-pri-miR-375 vector has the potential to be further explored in gene therapy for the treatment of HPV-caused cervical cancer.</div></div>","PeriodicalId":12499,"journal":{"name":"Gene","volume":"981 ","pages":"Article 149964"},"PeriodicalIF":2.4,"publicationDate":"2025-12-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145793765","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"In vitro expression and seroreactivity of Toxoplasma gondii GRA1 protein encoded by unmodified and nucleoside-modified mRNA constructs","authors":"Mehmet Nadir Şahinci ,&nbsp;Mert Döşkaya ,&nbsp;Muhammet Karakavuk ,&nbsp;Seren Kaplan ,&nbsp;Gizem Mutlu ,&nbsp;Tuğçe Gizem Perçin ,&nbsp;Sedef Erkunt Alak ,&nbsp;Özlem Günay-Esiyok ,&nbsp;Aytül Gül Mete ,&nbsp;Aysu Değirmenci Döşkaya ,&nbsp;Ayşe Gülten Kantarcı ,&nbsp;Adnan Yüksel Gürüz ,&nbsp;Hüseyin Can","doi":"10.1016/j.gene.2025.149965","DOIUrl":"10.1016/j.gene.2025.149965","url":null,"abstract":"<div><div>Toxoplasmosis is an infectious parasitic disease caused by <em>Toxoplasma gondii</em>, with a global seroprevalence estimated to affect more than one-third of the human population. <em>T. gondii</em> can be a serious health concern for pregnant women and immunocompromised patients. Currently, there is no effective and safe vaccine for humans. However, mRNA technology is a promising platform to develop efficient and safe vaccines against toxoplasmosis. Therefore, we designed nucleoside-modified and unmodified mRNA vaccine transcripts expressing <em>T. gondii</em> recombinant GRA1 protein and analyzed their <em>in vitro</em> protein expression profile as well as potential immunogenicity using IFAT, Western blot, and ELISA. Moreover, to compare translational efficiency, poly-A tail was extended with an extra ∼150 bp in addition to the existing ∼120 bp poly-A tail in two distinct mRNA designs. The results showed that all four mRNA constructs expressed rGRA1 protein in HEK293T cells. However, mRNA constructs with extended poly-A tails exhibited reduced expression level of rGRA1 protein compared to other mRNA vaccine transcripts. Additionally, unmodified mRNA construct with or without extended poly-A tail yielded significantly higher protein expression compared to nucleoside-modified mRNA constructs through ELISA using anti-polyhis antibody (P&lt;0.05). Western blot showed that rGRA1 protein expressed by all four mRNA constructs reacted strongly with <em>T. gondii</em> IgG seropositive mice sera. Furthermore, ELISA revealed that rGRA1 proteins derived from unmodified and nucleoside-modified mRNA constructs formed significantly stronger immune complexes with <em>T. gondii</em> IgG antibodies compared to negative controls (P&lt;0.05). These data suggest that both unmodified and nucleosidemodified mRNA constructs expressing rGRA1 protein have potential as vaccine candidates and warrant further investigation for development of an mRNA-based vaccine against toxoplasmosis. However, encapsulation of the produced mRNA constructs in LNPs and <em>in vivo</em> studies are required to validate these preliminary results.</div></div>","PeriodicalId":12499,"journal":{"name":"Gene","volume":"982 ","pages":"Article 149965"},"PeriodicalIF":2.4,"publicationDate":"2025-12-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145780138","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Under the dual hit: genetic and phenotypic analysis of a Han family with severe adolescent cirrhosis from the convergence of Wilson’s disease and favism","authors":"Yu-qin Xie ,&nbsp;Zi-yan Xu ,&nbsp;Hong Lin ,&nbsp;Li-jun Xie ,&nbsp;Jie-wei Luo ,&nbsp;Li-jun Zhang ,&nbsp;Zhi-hai Zheng","doi":"10.1016/j.gene.2025.149953","DOIUrl":"10.1016/j.gene.2025.149953","url":null,"abstract":"<div><div>Hepatolenticular degeneration (HLD, MIM:277900) is an autosomal recessive disorder characterized by excessive copper accumulation in hepatocytes, leading to hepatic and neurological abnormalities, hepatocellular injury, neurodegeneration, and copper deposition in the cornea. Glucose-6-phosphate dehydrogenase (G6PD) deficiency is the most common genetic cause of hemolytic anemia, which can be triggered by chronic conditions, drugs, food, or infections, and exhibits highly variable severity. In some cases, multiple genetic factors may collectively influence disease presentation and progression. This study reports a proband who developed abnormal liver function at age 20. Four years later, she exhibited severe jaundice, liver dysfunction, serous effusions, anemia, and Kayser–Fleischer rings, leading to diagnoses including decompensated cirrhosis, splenomegaly, suspected HLD, hemolytic anemia, portal hypertension, hypoproteinemia, low T3 syndrome, primary peritonitis, and gallstones with cholecystitis. Genetic screening identified two pathogenic heterozygous variants in ATP7B (NM_000053.4): c.2128G &gt; A (p.G710S) in exon 8 and c.525dupA (p.V176Sfs*28) in exon 2, together forming a compound heterozygous mutation. Additionally, a heterozygous mutation in G6PD (NM_001360016.2), c.1388G &gt; A (p.R463H) in exon 12, was found. Family members carrying the G6PD variant showed recurrent benign jaundice or remained asymptomatic. A heterozygous missense variant of uncertain significance, c.205C &gt; T (p.R69C), was also detected in exon 3 of STEAP3 (NM_182915.3), a gene linked to hypochromic microcytic anemia with iron overload type 2 (MIM#615234). This rare variant was predicted to be deleterious by in silico tools, suggesting possible genetic cosegregation.</div><div>SWISS-MODEL analysis indicated that these variants may alter the three-dimensional structures of the copper-transporting ATPase and G6PD proteins, potentially impairing function—particularly the frameshift mutation p.V176Sfs*28. We hypothesize that the accumulation of multiple pathogenic genetic factors resulted in a “double-hit” effect, leading to the patient’s severe phenotypes, including advanced liver cirrhosis and hemolytic anemia. Elucidating such multi-gene “double-hit” mechanisms may enhance the understanding of gene–gene interactions in complex diseases.</div></div>","PeriodicalId":12499,"journal":{"name":"Gene","volume":"981 ","pages":"Article 149953"},"PeriodicalIF":2.4,"publicationDate":"2025-12-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145780827","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Age-induced gene expression in Thoroughbred horse skeletal muscle highlights genes that enhance muscle architecture and function","authors":"Mian Feng ,&nbsp;Thomas J. Hall ,&nbsp;David E. MacHugh ,&nbsp;Lisa M. Katz ,&nbsp;Emmeline W. Hill","doi":"10.1016/j.gene.2025.149951","DOIUrl":"10.1016/j.gene.2025.149951","url":null,"abstract":"<div><div>Early skeletal muscle development is critical for young racehorses, yet research on the transcriptional changes during this period is limited. Additionally, the impact of age on the transcriptional response to exercise training in equine athletes is not well understood. A transcriptome-wide analysis of differential gene expression in skeletal muscle was performed for five untrained Thoroughbred horses sampled at rest at two years old (UR2) and three years old (UR3). A total of 136 differentially expressed genes (DEGs) were identified, with 95 increased and 41 decreased in expression. GO enrichment analysis revealed that the DEGs were primarily associated with terms related to muscle assembly and system development, including <em>Developmental process (GO:0032502</em>)<em>, Anatomical structure development (GO:0048856</em>)<em>, Actin cytoskeleton (GO:0015629</em>)<em>, and Growth factor binding (GO:0019838</em>)<em>.</em> KEGG pathway analysis indicated that <em>ECM-receptor interaction</em>, <em>Protein digestion and absorption</em>, <em>Focal adhesion</em>, and <em>PI3K-Akt signalling pathway</em> were the significant functional pathways. Protein-protein interaction network and hub gene analyses identified seven key regulatory genes: <em>COL1A1, COL1A2, COL3A1, S100A4, NOTCH1, THY1</em> and <em>MT-ND2.</em> In addition, the <em>MSTN, COL4A1, COL4A2, SPEN, S100A4, NOTCH1, NOTCH3, and THY1</em> genes were found to play key roles in the functional development of skeletal muscle. This study provides insight into the transcriptional landscape of skeletal muscle development in young Thoroughbred horses. The period between two and three years of age represents a crucial stage in skeletal muscle adaptation in the juvenile horse, with a particular emphasis on muscle structural and functional integrity.</div></div>","PeriodicalId":12499,"journal":{"name":"Gene","volume":"980 ","pages":"Article 149951"},"PeriodicalIF":2.4,"publicationDate":"2025-12-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145774290","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genetic and epigenetic determinants of injury risk and recovery in elite athletes: toward precision sports medicine","authors":"Hao Ding ,&nbsp;Qilu Deng ,&nbsp;Zhenhua Guo","doi":"10.1016/j.gene.2025.149957","DOIUrl":"10.1016/j.gene.2025.149957","url":null,"abstract":"<div><div>Musculoskeletal injuries and interindividual variability in recovery remain critical challenges for sustaining elite athletic performance. Despite advances in diagnostics, training, and rehabilitation, unexplained differences in injury risk and recovery efficiency persist. Growing evidence implicates genetic and epigenetic mechanisms in these disparities, influencing collagen integrity, inflammatory regulation, oxidative stress, and muscle regeneration. Key contributors include single-nucleotide polymorphisms (SNPs) in COL1A1, COL5A1, ACTN3, and IL6, as well as novel loci identified by genome-wide association studies (GWAS). Polygenic risk scores (PRS), which integrate the effects of multiple low-impact variants, enhance prediction compared to single-gene markers. Epigenetic regulators, including DNA methylation and exercise-responsive microRNAs (e.g., miR-206, miR-133a, miR-486), provide a dynamic interface linking genetic predisposition with environmental factors such as training load and nutrition. Integration of genomic data with wearable technologies and artificial intelligence enables real-time monitoring, adaptive recovery, and precision load management. Yet, clinical translation faces challenges including limited population diversity, interpretative complexity, and ethical concerns over data privacy and potential misuse. Advancing precision sports medicine will require multidisciplinary, systems-level strategies that unite molecular insights with practical implementation, ultimately enabling individualized injury prevention, optimized rehabilitation, and the preservation of long-term athlete health and performance.</div></div>","PeriodicalId":12499,"journal":{"name":"Gene","volume":"980 ","pages":"Article 149957"},"PeriodicalIF":2.4,"publicationDate":"2025-12-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145755941","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"SR protein kinase FoSrk1 integrates RNA splicing, carbon metabolism, and virulence in Fusarium oxysporum f. sp. cubense","authors":"Han Ouyang ,&nbsp;Jiayi Peng ,&nbsp;Zhouqi Huang ,&nbsp;Yicong Huang ,&nbsp;Yinglan Wen ,&nbsp;Yuan Xu ,&nbsp;Yu Long ,&nbsp;Huijiao Lin ,&nbsp;Qiyan Fu ,&nbsp;Zhaojian Ding","doi":"10.1016/j.gene.2025.149954","DOIUrl":"10.1016/j.gene.2025.149954","url":null,"abstract":"<div><div><em>Fusarium oxysporum</em> f. sp. <em>cubense</em> (Foc), the causal agent of banana Fusarium wilt, is one of the most destructive plant pathogens worldwide. However, the molecular mechanisms that integrate fungal growth, metabolism, and virulence remain poorly understood. This study identifies and functionally characterizes FoSrk1, a serine/arginine-rich protein kinase (SRPK), in Foc. Deletion of <em>FoSrk1</em> markedly impaired vegetative growth, reduced aerial mycelium formation and conidiation, and significantly attenuated virulence toward banana plantlets. The mutant also exhibited compromised utilization of diverse carbon sources, accompanied by altered expression of 32 genes involved in carbon metabolism. Complementation with the wild-type <em>FoSrk1</em> allele restored normal growth and pathogenicity, confirming the gene’s essential role. Transcriptomic analyses revealed that loss of <em>FoSrk1</em> altered the expression of 2,500 genes and was associated with changes in 37 alternative splicing events, predominantly intron retention, affecting transcripts linked to protein metabolism, ribosome biogenesis, and redox processes. Moreover, several virulence-associated genes encoding ABC transporters, cytochrome P450 enzymes, and hydrophobins were downregulated in the <em>FoSrk1</em>-deficient strain. These findings suggest that FoSrk1 acts as an important regulator that couples RNA processing with metabolic and pathogenic pathways and is required for normal fungal development and virulence. This study provides new insight into the molecular basis of pathogenic adaptation and identifies FoSrk1 as a potential target for antifungal intervention strategies.</div></div>","PeriodicalId":12499,"journal":{"name":"Gene","volume":"983 ","pages":"Article 149954"},"PeriodicalIF":2.4,"publicationDate":"2025-12-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145755939","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Two transcription factors and one antisense RNA underlie the thermoregulated insect pathogenicity of Yersinia entomophaga MH96","authors":"Amber R. Paulson ,&nbsp;Maureen O’Callaghan ,&nbsp;Xue-Xian Zhang ,&nbsp;Naran Naren ,&nbsp;Marion Schoof ,&nbsp;Mark R.H. Hurst","doi":"10.1016/j.gene.2025.149955","DOIUrl":"10.1016/j.gene.2025.149955","url":null,"abstract":"<div><div>Entomopathogenic bacteria express virulence genes in a temperature-dependent manner, but the underlying molecular mechanisms remain poorly understood. Here, we describe the roles of an unusual LytTR-containing transcription factor Yen6 in determining the virulence of <em>Yersinia entomophaga</em> (MH96). An initial transcriptome analysis <em>in vivo</em> revealed that <em>yen6</em>, located 1,372 bp upstream from genes encoding the Yen Toxin complex (Yen-Tc), exhibited significantly higher transcriptional activity at 37 °C compared to 25 °C (adjusted <em>p</em>-value &lt; 0.001) during intrahemocoelic infection in the insect model <em>Galleria‍ mellonella</em>. Deletion of <em>yen6</em> also significantly reduced MH96′s virulence in <em>G.‍‍ mellonella</em> by up to three-fold. Next, comparing the transcriptome of wild-type MH96 and its derived Δ<em>yen6</em> mutant revealed genes for ribose utilization were downregulated whereas genes for fructose utilization and the RNA-binding protein YhbY were upregulated in the <em>yen6-</em>deficient mutant. Subsequent electromobility shift assays showed that purified Yen6_His6 protein was capable of specifically binding to the promoter regions of the ribose and fructose utilization-related gene clusters, as well as <em>yhbY</em>. A 645-nucleotide-long 3′ untranslated region, designated <em>yen7_AS</em>, was identified extending from the <em>yen6</em> coding region. Notably, <em>yen7_AS</em> completely overlaps the <em>yen7</em> gene on the opposing strand and may therefore act as a <em>cis</em> anti-sense RNA regulating <em>yen7</em> expression, which encodes a putative transcriptional regulator of the Yen-Tc. This study highlights the critical role of the <em>yen6–yen7</em> locus in MH96 virulence during <em>G.‍ mellonella</em> infection<em>,</em> including the complex mechanisms controlling insecticidal exoprotein production.</div></div>","PeriodicalId":12499,"journal":{"name":"Gene","volume":"980 ","pages":"Article 149955"},"PeriodicalIF":2.4,"publicationDate":"2025-12-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145752086","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genome-wide association study of tolerance to acute hypoxia in the olive flounder (Paralichthys olivaceus) using individual blood cortisol levels as a physiological phenotype","authors":"M.A.H. Dilshan ,&nbsp;Gaeun Kim ,&nbsp;W.K.M. Omeka ,&nbsp;D.S. Liyanage ,&nbsp;H.M.V. Udayantha ,&nbsp;D.C.G. Rodrigo ,&nbsp;G.A.N.P. Ganepola ,&nbsp;H.A.C.R. Hanchapola ,&nbsp;Y.K. Kodagoda ,&nbsp;Po Gong ,&nbsp;Jihun Lee ,&nbsp;Sukkyoung Lee ,&nbsp;Jeongeun Kim ,&nbsp;Jehee Lee","doi":"10.1016/j.gene.2025.149952","DOIUrl":"10.1016/j.gene.2025.149952","url":null,"abstract":"<div><div>Hypoxia, caused by reduced dissolved oxygen (DO) levels in water, is a critical challenge in aquaculture and often results in stress, anorexia, and mass mortality in fish. The olive flounder (<em>Paralichthys olivaceus</em>) is a key species in South Korea’s global aquaculture exports. However, aquaculture production of <em>P. olivaceus</em> experiences significant economic losses caused by hypoxia-induced fish mortality, highlighting the critical need for developing genetically improved hypoxia-tolerant strains. In this study, a genome-wide association study (GWAS) was performed to unveil single-nucleotide polymorphisms (SNPs) associated with acute hypoxia tolerance and elucidate underlying regulatory mechanisms. A total of 382 <em>P. olivaceus</em> fish were measured for blood serum cortisol level using enzyme-linked immunosorbent assay (ELISA) upon acute hypoxia stress. Blood plasma cortisol levels were used as a proxy phenotype of hypoxia tolerance, with the hypothesis that elevated concentrations indicate low tolerance, and minimized concentrations indicate high tolerance to acute hypoxia stress. Then, fish were genotyped using the Affymetrix® Axiom® myDesign™ genotype array, and 57,651 SNPs were retained after quality control filtering. A significant SNP was identified on chromosome 15 of the <em>P. olivaceus</em> genome, above the suggestive threshold (<em>p</em> &lt; 1 × 10⁻⁴) for the stress cortisol level trait. A strongly associated SNP with accession number AX-419149718 was located in the zona pellucida-like domain-containing protein 1 (<em>Zpld1</em>) gene. Gene ontology (GO) analysis suggests that <em>Zpld1</em> is involved in signaling pathways, including the integrin-mediated signaling pathway, thereby contributing to the mitigation of hypoxia stress effects. Collectively, this study provides insights into the genetic basis of acute hypoxia tolerance in <em>P. olivaceus</em> and may serve as a foundation for establishing genomic selection of olive flounders with acute hypoxia stress tolerance in aquaculture breeding programs.</div></div>","PeriodicalId":12499,"journal":{"name":"Gene","volume":"980 ","pages":"Article 149952"},"PeriodicalIF":2.4,"publicationDate":"2025-12-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145735922","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Differential genomic signatures of homozygosity and a haplotype sharing Extents across breeds associated with body size variation in Korean indigenous goats","authors":"Seongmin Kim ,&nbsp;Hankyeol Jeong ,&nbsp;Ga-Eun Kim ,&nbsp;Kwan-Woo Kim ,&nbsp;Woncheoul Park ,&nbsp;Jaemin Kim ,&nbsp;Bong-Hwan Choi","doi":"10.1016/j.gene.2025.149956","DOIUrl":"10.1016/j.gene.2025.149956","url":null,"abstract":"<div><div>Korean indigenous goats are maintained as purebred lineages in geographically isolated populations such as Dangjin, Gyeongsang National University (GNU), Jangsu, and Tongyeong. However, their small population size and high rates of inbreeding have raised concerns regarding the preservation of genetic diversity. We generated SNP genotypes for 217 Korean indigenous goats using the GoatSNP50 BeadChip, and standardized body size measurements with complete metadata were available for 64 adult individuals. Principal component analysis (PCA) clearly separated the four lineages, with the GNU population showing particularly high values of inbreeding coefficient and proportion of runs of homozygosity, reflecting the impact of recent closed breeding. Genome-wide patterns of haplotype sharing revealed exploratory trends suggesting that introgression from global breeds tended to coincide with larger body size, whereas intensified inbreeding within the Korean population showed a general tendency toward reduced body size. Furthermore, cross-population extended haplotype homozygosity (XP-EHH) analysis revealed candidate genes, including <em>ADGRL3</em>, <em>SP8</em>, and <em>ARL6IP5</em> that are likely involved in adaptation to seasonal environmental stress. Our findings highlight the global connectivity, functional relevance of body conformation traits, and selective signatures of Korean indigenous goats, providing a genomic foundation for preserving diversity and guiding future breeding.</div></div>","PeriodicalId":12499,"journal":{"name":"Gene","volume":"980 ","pages":"Article 149956"},"PeriodicalIF":2.4,"publicationDate":"2025-12-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145752089","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Inorganic nitrogen sources and light cooperatively stimulate gene regulation for non-photosynthetic phosphoenolpyruvate carboxylase in wheat leaves","authors":"Naoki Yamamoto ,&nbsp;Jingru Jiang ,&nbsp;Haoyu Deng ,&nbsp;Ken-ichi Kurotani ,&nbsp;Jiang Zou ,&nbsp;Zaijun Yang","doi":"10.1016/j.gene.2025.149950","DOIUrl":"10.1016/j.gene.2025.149950","url":null,"abstract":"<div><div>Phospho<em>enol</em>pyruvate carboxylase (PEPC) is a bicarbonate fixation enzyme that is associated with nitrogen metabolism. We previously observed that NO₃^– affected the expression levels of <em>PEPC</em> genes differently in detached wheat leaves. Three types of <em>PEPC</em> isogenes, including the orthologous isogene group (<em>Tappc1b</em>) for C₄-photosynthetic <em>PEPC</em>, exhibited distinct transcriptionally up-regulated patterns from one another. However, it remains unclear which nitrogen compounds exactly trigger the gene expression responses and their light dependency. Here, we investigated the cause of isogene-specific expression responses of <em>PEPCs</em> to different forms of nitrogen supplementation. Detached leaves from wheat seedlings cultivated under a nitrogen-deficient condition were incubated with NO₃^–, NH₄⁺, and urea under both light and dark conditions. Notably, the genes analyzed exhibited markedly different expression patterns across the nitrogen forms under the light condition. <em>Tappc1a</em>, which did non-respond to NO₃^–, was up-regulated by NH₄⁺ exclusively under light. <em>Tappc2</em> was also up-regulated by NO₃^– and NH₄⁺ only under light, and these up-regulations were suppressed under the dark condition. The candidate transcriptional regulator <em>DOF1</em> for <em>Tappc1b</em> in wheat was also up-regulated by NO₃^– only under light condition, but earlier than <em>Tappc1b</em>, implicating a DOF1-mediated transcriptional response of <em>Tappc1b</em> to NO₃^–. Comparison of <em>Tappc1b</em> promoter sequences with that of NO₃^–-responsive maize C₄ <em>PEPC</em> revealed conserved light-responsive elements near the Dof1 binding site. These findings suggest that distinct transcriptional regulatory cascades would exist for non-photosynthetic <em>PEPCs</em> in response to different inorganic nitrogen forms.</div></div>","PeriodicalId":12499,"journal":{"name":"Gene","volume":"980 ","pages":"Article 149950"},"PeriodicalIF":2.4,"publicationDate":"2025-12-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145741963","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}