Functional & Integrative Genomics最新文献

{"title":"High expression of formin-2 can promote ovarian cancer chemoresistance via immunosuppressive macrophages","authors":"Shuo Feng,&nbsp;Yaping Wang,&nbsp;Ran Ren,&nbsp;Xiaotong Wang,&nbsp;Lu Han","doi":"10.1007/s10142-025-01766-z","DOIUrl":"10.1007/s10142-025-01766-z","url":null,"abstract":"<div><p>Ovarian cancer (OC) remains a major threat to women’s health, with chemoresistance driven by the immunosuppressive tumor microenvironment. Formin-2 (FMN2), a cytoskeletal regulator, was investigated for its role in OC chemoresistance and macrophage polarization. Bioinformatics analysis identified high FMN2 expression in chemotherapy-resistant OC cell lines, validated experimentally. Stable FMN2 knockdown cell lines were generated via lentiviral transfection. Functional assays revealed that FMN2 overexpression conferred chemoresistance in vitro and in vivo and promoted M2 macrophage polarization via the CCL2/JAK2/STAT3 pathway. Co-culture with M2 macrophages enhanced cisplatin (DDP) resistance in OC cells, mediated by CXCL1 secretion, which activated the epithelial-mesenchymal transition (EMT) pathway. Clinically, FMN2 levels correlated with CCL2 and CD206 (M2 marker) in platinum-resistant patients, and high FMN2, CCL2, or CD206 expression predicted poorer overall and disease-free survival. This study identifies FMN2 as a key mediator of chemoresistance and immune evasion in OC, proposing FMN2-CCL2-CD206 signaling and macrophage-derived CXCL1 as therapeutic targets and prognostic markers for chemotherapy response.</p></div>","PeriodicalId":574,"journal":{"name":"Functional & Integrative Genomics","volume":"26 1","pages":""},"PeriodicalIF":3.1,"publicationDate":"2025-12-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145779331","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Gastrodin extends the lifespan of Caenorhabditis elegans via the DAF-16/FOXO signaling pathway and autophagy","authors":"Bo Li,&nbsp;Shan Li,&nbsp;Haoling Chen,&nbsp;Dan Wu,&nbsp;Xingwang Cao,&nbsp;Mingyue Yao,&nbsp;Shiying Xiong,&nbsp;Wei Meng,&nbsp;Li Dong","doi":"10.1007/s10142-025-01771-2","DOIUrl":"10.1007/s10142-025-01771-2","url":null,"abstract":"<div>\u0000 \u0000 <p>The progression of age-related pathologies is strongly linked to biological aging. Identifying natural anti-aging agents to mitigate disease onset and development holds substantial therapeutic value. The natural compound Gastrodin (Gas) demonstrates promising effects in retarding aging. This study aims to explore the effects of Gas on the lifespan and antioxidant capacity of <i>Caenorhabditis elegans (C. elegans)</i>. Additionally, it seeks to elucidate the possible mechanisms. Initially, Gas was assessed for its influence on <i>C. elegans</i> lifespan, mobility, lipofuscin accumulation, and oxidative stress responses. Subsequent analyses focused on Gas’s modulation of the insulin/IGF-1 pathway, mitochondrial activity, autophagic processes, and gene expression to uncover its lifespan-extending mechanisms. Gas induced a dose-dependent lifespan extension in <i>C. elegans</i>, peaking at 400 µM with a 17.3% increase in longevity. Gas enhanced <i>C. elegans</i> mobility while suppressing age-related lipofuscin deposition.Additionally, Gas lowered ROS levels and elevated antioxidant enzyme activity in <i>C. elegans</i>.Mechanistic studies revealed that Gas’s anti-aging effects rely on transcription factors (DAF-16, SKN-1, HSF-1) and bolster stress resistance via HSPs activation and autophagy induction. This study reveals the potential of Gas in extending the lifespan of <i>C. elegans</i>, emphasizes its mechanism of action by regulating antioxidant capacity, heat stress response, and autophagy pathway, and provides experimental evidence that supports the development of Gas as a candidate compound for lifespan extension.</p>\u0000 </div>","PeriodicalId":574,"journal":{"name":"Functional & Integrative Genomics","volume":"26 1","pages":""},"PeriodicalIF":3.1,"publicationDate":"2025-12-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145773260","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Candidate genes for anthracnose resistance in Senegalese sorghum: a machine learning-based exploration","authors":"Ezekiel Ahn,&nbsp;Insuck Baek,&nbsp;Louis K. Prom,&nbsp;Sunchung Park,&nbsp;Moon S. Kim,&nbsp;Lyndel W. Meinhardt,&nbsp;Clint Magill","doi":"10.1007/s10142-025-01797-6","DOIUrl":"10.1007/s10142-025-01797-6","url":null,"abstract":"<div><p>Anthracnose, caused by the hemibiotrophic fungal pathogen <i>Colletotrichum sublineola</i>, is a significant constraint to sorghum production worldwide. Developing resistant cultivars is the most sustainable control strategy, but it requires constant additional sources of resistance genes. Here, we applied machine learning (ML) approaches, specifically Bootstrap Forest and Boosted Tree models, to identify single-nucleotide polymorphisms (SNPs) associated with anthracnose resistance in a panel of Senegalese sorghum accessions using publicly available phenotypic data from seedling and 8-leaf stages. The ML models identified five novel high-importance loci distinct from those found by linear model-based Genome-wide association studies (GWAS), while also reinforcing three candidates detected by both methods. The top candidates found through ML algorithms were leucine-rich repeat (LRR), F-box, aspartic peptidase, and jasmonate O-methyltransferase. Several genes were highlighted by both ML and GWAS, strengthening the evidence for their involvement. This study demonstrates the potential of ML to complement traditional GWAS in identifying candidate genes for complex traits, providing a valuable resource for future functional studies and marker-assisted selection efforts to enhance anthracnose resistance in sorghum. Given the constraints of the available population size, these results are best interpreted as an explanatory framework that highlights potential targets for further investigation and guides future functional validation, rather than as a definitive predictive tool.</p></div>","PeriodicalId":574,"journal":{"name":"Functional & Integrative Genomics","volume":"26 1","pages":""},"PeriodicalIF":3.1,"publicationDate":"2025-12-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s10142-025-01797-6.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145773221","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Overcoming barriers in CAR-NK immunotherapy: CRISPR-Driven advances in checkpoint editing and allogeneic design","authors":"Mohammed J. Mansoor,&nbsp;Sarah F. Al-Taie,&nbsp;Zahraa Abbas Al-Khafaji,&nbsp;Ali G. Alkhathami,&nbsp;Jyothi S. Renuka,&nbsp;Rajashree Panigrahi,&nbsp;Hansi Negi,&nbsp;Pushkar Jassal,&nbsp;Yasser Fakri Mustafa,&nbsp;Hamza Fadhel Hamzah","doi":"10.1007/s10142-025-01778-9","DOIUrl":"10.1007/s10142-025-01778-9","url":null,"abstract":"<div>\u0000 \u0000 <p>Chimeric antigen receptor (CAR)-engineered natural killer (NK) cells are emerging as an exciting avenue in cancer immunotherapy due to their potent cytotoxicity to malignant cells and lower risk of graft-versus-host disease (GvHD) than conventional T cell therapies. The new technology of CRISPR/Cas9 genome editing has significantly expedited the engineering of CAR-NK cells by enabling easy, multiplex, and precise changes to enhance their efficacy, persistence, and specificity to tumors. This review focuses on the incorporation of CRISPR technology into CAR-NK cell development. It examines uses of knockout of inhibitory checkpoint genes (<i>CISH</i>,<i> PD-1</i>, and <i>TGFBR2</i>), as well as knock-in of CAR into safe genomic locations and multiplex editing of CAR-NK cells to improve cytotoxicity against cancer while resisting suppression from the tumor microenvironment (TME). We further explore immuno-cytokine armoring strategies by knock-in of <i>IL-15</i> or <i>IL-12</i>, to ensure prolonged proliferation and survival of NK cells, and investigate CRISPR-mediated knockouts of immune inhibitors like <i>NKG2A</i> and <i>TIGIT</i>, to evade immune strategies used by the tumor to evade immune destruction. Furthermore, CRISPR-mediated upregulation of the homing receptor enhances NK cell tumor infiltration, addressing a major obstacle in treating solid tumors. It is significant to mention the progress in generating off-the-shelf products, which is a key step supporting the pursuit of allogeneic therapies. While substantial progress has been made, challenges remain related to optimizing CRISPR delivery, off-target effects, and enhancing in vivo persistence. Future directions of CAR-NK studies will likely capitalize on next-generation genome editing tools and synthetic biology for the development of tunable and logic-gated CAR-NK cells. Overall, this review illustrates the revolutionary capacity of combining CRISPR technology with CAR-NK immunotherapy to develop next-generation programmable and efficacious treatments for hematologic and solid malignancies.</p>\u0000 </div>","PeriodicalId":574,"journal":{"name":"Functional & Integrative Genomics","volume":"26 1","pages":""},"PeriodicalIF":3.1,"publicationDate":"2025-12-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145766815","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The application of RPA-PfAgo technology combined with multidimensional data analysis in the rapid detection of the MTHFR A1298C polymorphism","authors":"Yaqun Liu,&nbsp;Lianghui Chen,&nbsp;Xuanyi Zheng,&nbsp;Peikui Yang,&nbsp;Jinkun Han,&nbsp;Jiayi Huang,&nbsp;Yanling Shen,&nbsp;Xiaotong Cai,&nbsp;Miaofen Fang,&nbsp;Yicun Chen,&nbsp;Chengsong Xie,&nbsp;Min Lin,&nbsp;Yuzhong Zheng","doi":"10.1007/s10142-025-01800-0","DOIUrl":"10.1007/s10142-025-01800-0","url":null,"abstract":"<div><p>This study presents a novel approach that integrates recombinase polymerase amplification (RPA) with <i>Pf</i>Ago protein technology for the rapid and precise detection of the <i>MTHFR</i> A1298C polymorphism. Although traditional genotyping methods are effective, they are often limited by complexity, high cost, and the need for specialized equipment. The RPA-<i>Pf</i>Ago technique harnesses the swift isothermal amplification of RPA and the high specificity and sensitivity of <i>Pf</i>Ago-mediated DNA cleavage, completing the entire process from sample collection to detection within 90 min. The utility of this method has been substantiated through a battery of optimization experiments, parameter analysis, and assessments of sensitivity, specificity, and repeatability, along with clinical validation using oral mucosal samples. These findings indicate that this new technology not only substantially reduces detection time and cost but also offers an effective tool for personalized medicine and disease prevention with high accuracy and reliability.</p></div>","PeriodicalId":574,"journal":{"name":"Functional & Integrative Genomics","volume":"26 1","pages":""},"PeriodicalIF":3.1,"publicationDate":"2025-12-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145761827","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Sequence dynamics and plastome evolution: decoding the complete chloroplast genome of Oenothera drummondii and comparative analysis within Oenothera (Onagraceae)","authors":"Chang An,&nbsp;Wenbo Xu,&nbsp;Yixin Yao,&nbsp;Min Li,&nbsp;Yanxiang Lin,&nbsp;S. V. G. N. Priyadasrhani,&nbsp;Aya Elderini,&nbsp;Yan Cheng,&nbsp;Site Luo,&nbsp;Yuan Qin,&nbsp;Ping Zheng","doi":"10.1007/s10142-025-01752-5","DOIUrl":"10.1007/s10142-025-01752-5","url":null,"abstract":"<div><p>Oenothera species are increasingly valued for their medicinal and ornamental qualities and serve as important models in classical cytoplasmic genetics research. The genus <i>Oenothera</i> L., one of the largest in the Onagraceae family, includes 18 subsections and two deep phylogenetic lineages, Clade A and Clade B. Analyzing high-quality chloroplast genomes can provide crucial insights into species classification and genus-level evolution. In this study, we report the complete chloroplast genome of <i>Oenothera drummondii</i> Hook., the first species from subsection <i>Raimannia</i>, with a total length of 167,177 bp and a GC content of 39.3%. This genome contains 129 genes and displays a typical quadripartite structure. Combining this genome with data from 16 publicly available chloroplast genomes, we conducted a comprehensive comparative and evolutionary analysis. Our results indicate that Clade B species diverged independently from Clade A species. Within Clade A, species from subsection <i>Muniza</i> form a distinct branch, while <i>O. drummondii</i> clusters closely with species from subsection <i>Oenothera</i>. Phylogenetic analysis correlates well with chloroplast genome structural differences, such as the loss of the <i>infA</i> gene in Clade B species, the expansion of the IR regions in <i>Muniza</i>, and a shared large inversion in the LSC region among <i>Raimannia</i> and <i>Oenothera</i> species. We also identified repeat sequences, six highly variable genes, and positively selected genes among the 17 chloroplast genomes analyzed. These findings offer valuable insights into the evolutionary processes of <i>Oenothera</i> species and provide a foundation for the development of future molecular markers based on the identified genes and structural variations.</p><h3>Graphical Abstract</h3><div><figure><div><div><picture><source><img></source></picture></div></div></figure></div></div>","PeriodicalId":574,"journal":{"name":"Functional & Integrative Genomics","volume":"26 1","pages":""},"PeriodicalIF":3.1,"publicationDate":"2025-12-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145729859","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Transgenic gamete cleaning system enabled high-throughput screening for non-transgenic gene-edited plants","authors":"Shifei Sang,&nbsp;Mengru Liu,&nbsp;Tian Tian,&nbsp;Shiqian Zhang","doi":"10.1007/s10142-025-01782-z","DOIUrl":"10.1007/s10142-025-01782-z","url":null,"abstract":"<div><p>The breakthrough progress in gene editing technology has established a brand-new paradigm for gene function analysis and crop genetic improvement, and has already become the core driving force in modern agricultural biotechnology. However, traditional methods for screening edited individual plants without T-DNA insertion in their offspring are time-consuming and labor-intensive. To accelerate the identification of T-DNA-free edited plants, researchers have continuously explored various strategies to improve screening efficiency, achieving some success. Despite this progress, these strategies also exhibit varying degrees of limitations. Recently, research teams led by Cheng and Sun (2025) and Zhu et al. (2025) constructed gamete elimination systems, successfully achieving a 100% non-transgenic status in the mutant plants. This innovative approach has transformed traditional molecular testing from a \"laboratory-dependent\" model to \"field-based real-time decision-making\" providing an efficient and cost-effective solution for precision breeding.</p></div>","PeriodicalId":574,"journal":{"name":"Functional & Integrative Genomics","volume":"26 1","pages":""},"PeriodicalIF":3.1,"publicationDate":"2025-12-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145719330","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Analyses of gene families, allelic variation and VIGS reveal that GheIF3M.2 is significantly associated with dwarfism and the absence of flower buds in upland cotton","authors":"Dandan Li,&nbsp;Xueli Zhang,&nbsp;Junning Yang,&nbsp;Xuefeng Guo,&nbsp;Ying Li,&nbsp;Qiwen Yang,&nbsp;Wenmin Yuan,&nbsp;Tingting Zhang,&nbsp;Caixiang Wang,&nbsp;Jian Li,&nbsp;Junji Su","doi":"10.1007/s10142-025-01773-0","DOIUrl":"10.1007/s10142-025-01773-0","url":null,"abstract":"<div>\u0000 \u0000 <p>Eukaryotic translation initiation factor 3 (eIF3), the largest eukaryotic initiation factor, regulates mRNA translation initiation. While eIF3 has been extensively studied in various plant species, research on eIF3 in upland cotton remains limited. A total of 60 <i>GheIF3s</i> were identified using a bioinformatics approach, and comprehensive characteristic analysis was conducted in upland cotton. The results revealed that the different subunits of the <i>GheIF3s</i> were strongly conserved in both structural and evolutionary relationships. RNA-seq and qRT‒PCR results revealed that the expression levels of <i>GheIF3L.1</i> and <i>GheIF3M.2</i> in early‒maturing varieties were significantly greater than those in late-maturing varieties. Furthermore, no single-nucleotide polymorphisms (SNPs) were detected in <i>GheIF3L.1</i>, and a SNP (A05:105181831, T/G) significantly related to the flowering period within the coding sequence of <i>GheIF3M.2</i> was identified. The flowering time of the varieties carrying the GG allele was significantly earlier than that of the varieties carrying the TT allele, which was verified in both early − flowering and late-flowering varieties via Sanger sequencing. Genetic diversity analysis revealed that the gene region differed between early − and late − maturing varieties. Virus-induced gene silencing (VIGS) results indicated that the silenced plants (TRV:<i>GheIF3M.2</i>) presented a significant decrease in plant height; inhibited flower bud differentiation; and significantly decreased IAA, GA₃, and BR contents. These analyses elucidated the functions of <i>GheIF3s</i> in upland cotton and provided genetic resources related to plant morphology and early maturity.</p>\u0000 </div>","PeriodicalId":574,"journal":{"name":"Functional & Integrative Genomics","volume":"25 1","pages":""},"PeriodicalIF":3.1,"publicationDate":"2025-12-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145720233","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genetic evaluation of CRISPR-Cas9 off-target effects from deleterious mutations on Drosophila male single X chromosome","authors":"Wei Bian,&nbsp;David W. J. Mcquarrie,&nbsp;Irmgard U. Haussmann,&nbsp;Roland Arnold,&nbsp;Matthias Soller","doi":"10.1007/s10142-025-01775-y","DOIUrl":"10.1007/s10142-025-01775-y","url":null,"abstract":"<div><p>Clustered regularly interspaced short palindromic repeats (CRISPR)-associated nuclease protein 9 (Cas9) is a powerful tool used for genome engineering, but concerns remain about off-target effects. Here we evaluate potential deleterious effects of CRISPR-Cas9 by combining sequence analysis and the genetics of the male X chromosome in a <i>Drosophila</i> model. Since males have only one X chromosome deleterious mutations on the X chromosome will manifest in reducing viability or result in visible phenotypes and thus provide sensitive readouts of off-target activity. Our data do not support large scale off-target effects in <i>Drosophila</i>. To optimize sgRNA selection, we incorporated off-target evaluation into the PlatinumCRISPr sgRNA selection tool for a broad range of organisms.</p></div>","PeriodicalId":574,"journal":{"name":"Functional & Integrative Genomics","volume":"25 1","pages":""},"PeriodicalIF":3.1,"publicationDate":"2025-12-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s10142-025-01775-y.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145712976","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"CRISPR/Cas9-mediated generation of GATA3 knockout in Bovine Fibroblast and MDBK cell lines to assess sgRNAs targeting efficiency","authors":"Qurat Ul Ain,&nbsp;Afshan McCarthy,&nbsp;Asif Nadeem,&nbsp;Maryam Javed,&nbsp;Kathy Niakan,&nbsp;Ali Fouladi Nashta","doi":"10.1007/s10142-025-01774-z","DOIUrl":"10.1007/s10142-025-01774-z","url":null,"abstract":"<div><p><i>GATA3</i> is expressed in the outer cells of the morula stage during embryonic development and is considered a key driver of the regulation of early lineage development in bovines. This research presents an optimised somatic cell validation resource, successfully generating <i>GATA3</i> knockout (KO) Bovine Fetal Fibroblasts and MDBK cells using CRISPR/Cas9-mediated genome editing for their future implications in vivo studies designed to definitively understand the role of <i>GATA3</i> in cell lineage specification and bovine embryo development. This involved designing single-guide RNAs (sgRNAs) targeting different regions of the <i>GATA3</i> gene, cloning them into the px459 plasmid, delivering the CRISPR clone into bovine fibroblast cells and the MDBK cell line, screening for successful targeting and knockouts, and MiSeq analysis to verify successful disruption of the <i>GATA3</i> gene. A total of eleven guides were designed targeting the functional domains in Exons 4 and 5 and the transcription initiation site in Exon 2. Designed guides were first optimized and screened using an in vitro cleavage assay. The guides with the best cutting efficiencies were then tested in vivo by targeting bovine fetal fibroblast (BFFs) and MDBK cell line followed by MiSeq analysis to verify the successful knockouts. A total of two effective guides were identified targeting the zinc-finger (ZnF) functional domains of the <i>GATA3</i> gene (sgRNA#5 and sgRNA#8 in Exon 4 and Exon 5, respectively) and one in Exon 2 (sgRNA#1) targeting the transcription initiation site of the <i>GATA3</i> gene. MiSeq data from targeted bovine cells showed indel frequency of 47.40%, 55.5%, and 42.4% in bovine fetal fibroblasts, 11.03%, 28.9% and 7.3% for MDBK cells for top three sgRNAs. Overall, MiSeq data for 3 selected sgRNAs showed successful disruption of the <i>GATA3</i> gene, inserting a base pair 2–3 bp upstream of the PAM site, ultimately resulting in a premature stop codon TAA in the downstream region. This study established and validated highly efficient sgRNAs targeting the <i>GATA3</i> gene, forming a molecular basis for forthcoming functional investigations in bovine embryos to explore gene function and protein-level effects.</p></div>","PeriodicalId":574,"journal":{"name":"Functional & Integrative Genomics","volume":"25 1","pages":""},"PeriodicalIF":3.1,"publicationDate":"2025-12-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145707060","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}