Genes & genomics最新文献

{"title":"Distinct granzyme k expression in immune cells: a single-cell rna-seq meta-analysis.","authors":"Hyeon-Young Kim, Hongseok Ha","doi":"10.1007/s13258-024-01555-1","DOIUrl":"10.1007/s13258-024-01555-1","url":null,"abstract":"<p><strong>Background: </strong>Granzymes are essential serine proteases in cytotoxic T cells and natural killer (NK) cells, with GZMK's expression being less understood. This study aims to uncover GZMK expression profiles across various immune cell types using single-cell RNA sequencing meta-analysis.</p><p><strong>Objective: </strong>This study aims to uncover GZMK expression profiles across various immune cell types using single-cell RNA sequencing meta-analysis.</p><p><strong>Methods: </strong>We conducted a meta-analysis using cellxgene, an interactive data exploration platform developed by the Chan Zuckerberg Initiative. We focused on mature T cells, NK cells, B cells, and NKT cells. We also checked transcription factor binding sites at the granzyme gene promoter regions using JASPAR. Comparative analysis was also done using mouse single-cell RNA sequencing data.</p><p><strong>Results: </strong>GZMK was the most lowly expressed in NK cells and mature NKT cells in most tissues except for colon and lymph nodes. In mature T cells, GZMK is similarly or more highly expressed than other granzymes. HBCA data revealed weak expression of GZMK in NK cells but strong expression in effector memory CD8-positive, alpha-beta T cells. Combined data shows no significant difference in GZMK expression between cell types. Subtype analysis shows that GZMK expression was higher in CD16-negative, CD56-bright NK cells when compared to CD16-positive, CD56-dim NK cells. We also identified unique transcription factor binding sites for GZMK. While this pattern in mouse data with low Gzmk expression in NK cells and higher T cells was repeated.</p><p><strong>Conclusion: </strong>GZMK expression is distinctively regulated among immune cells and tissues, with unique promoter regions and transcription factor binding sites contributing to this differential expression. These insights into GZMK's role in immune function and regulation offer potential therapeutic targets.</p>","PeriodicalId":12675,"journal":{"name":"Genes & genomics","volume":null,"pages":null},"PeriodicalIF":1.6,"publicationDate":"2024-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141901448","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":"Analysis of single-cell transcriptome data from a mouse model implicates protein synthesis dysfunction in schizophrenia.","authors":"Andrew E Weller, Thomas N Ferraro, Glenn A Doyle, Benjamin C Reiner, Wade H Berrettini, Richard C Crist","doi":"10.1007/s13258-024-01545-3","DOIUrl":"10.1007/s13258-024-01545-3","url":null,"abstract":"<p><strong>Background: </strong>Schizophrenia is a mental disorder that causes considerable morbidity, whose risk largely results from genetic factors. Setd1a is a gene implicated in schizophrenia.</p><p><strong>Objective: </strong>To study the gene expression changes found in heterozygous Setd1a^± knockout mice in order to gain useful insight into schizophrenia pathogenesis.</p><p><strong>Methods: </strong>We mined a single-cell RNA sequencing (scRNAseq) dataset from the prefrontal cortex (PFC) and striatum of Setd1a^± mice and identified cell type-specific differentially expressed genes (DEGs) and differential transcript usage (DTU). DEGs and genes containing DTU found in each cell type were used to identify affected biological pathways using Ingenuity Pathway Analysis (IPA).</p><p><strong>Results: </strong>We identified 273 unique DEGs across all cell types in PFC and 675 unique gene peaks containing DTU. In striatum, we identified 327 unique DEGs across all cell types and 8 unique gene peaks containing DTU. Key IPA findings from the analysis of DEGs found in PFC and striatum implicate processes involved in protein synthesis, mitochondrial function, cell metabolism, and inflammation. IPA analysis of genes containing DTU in PFC points to protein synthesis, as well as cellular activities involving intracellular signaling and neurotransmission. One canonical pathway, 'EIF2 Signaling', which is involved in the regulation of protein synthesis, was detected in PFC DEGs, striatum DEGs, and PFC genes containing DTU, drawing attention to its importance in schizophrenia pathophysiology.</p><p><strong>Conclusion: </strong>Processes involving protein synthesis in general and the 'EIF2 Signaling' pathway in particular could be targets for the development of new research strategies and biomarkers in schizophrenia.</p>","PeriodicalId":12675,"journal":{"name":"Genes & genomics","volume":null,"pages":null},"PeriodicalIF":1.6,"publicationDate":"2024-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141855334","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":"Actn2 defects accelerates H9c2 hypertrophy via ERK phosphorylation under chronic stress.","authors":"Kang Wang, Ye Wang, Hua Wan, Jie Wang, Li Hu, Shuainan Huang, Mingchen Sheng, Jiayi Wu, Xing Han, Youjia Yu, Peng Chen, Feng Chen","doi":"10.1007/s13258-024-01536-4","DOIUrl":"10.1007/s13258-024-01536-4","url":null,"abstract":"<p><strong>Background: </strong>In humans, ACTN2 mutations are identified as highly relevant to a range of cardiomyopathies such as DCM and HCM, while their association with sudden cardiac death has been observed in forensic cases. Although ACTN2 has been shown to regulate sarcomere Z-disc organization, a causal relationship between ACTN2 dysregulation and cardiomyopathies under chronic stress has not yet been investigated.</p><p><strong>Objective: </strong>In this work, we explored the relationship between Actn2 dysregulation and cardiomyopathies under dexamethasone treatment.</p><p><strong>Methods: </strong>Previous cases of ACTN2 mutations were collected and the conservative analysis was carried out by MEGA 11, the possible impact on the stability and function of ACTN2 affected by these mutations was predicted by Polyphen-2. ACTN2 was suppressed by siRNA in H9c2 cells under dexamethasone treatment to mimic the chronic stress in vitro. Then the cardiac hypertrophic molecular biomarkers were elevated, and the potential pathways were explored by transcriptome analysis.</p><p><strong>Results: </strong>Actn2 suppression impaired calcium uptake and increased hypertrophy in H9c2 cells under dexamethasone treatment. Concomitantly, hypertrophic molecular biomarkers were also elevated in Actn2-suppressed cells. Further transcriptome analysis and Western blotting data suggested that Actn2 suppression led to the excessive activation of the MAPK pathway and ERK cascade. In vitro pharmaceutical intervention with ERK inhibitors could partially reverse the morphological changes and inhibit the excessive cardiac hypertrophic molecular biomarkers in H9c2 cells.</p><p><strong>Conclusion: </strong>Our study revealed a functional role of ACTN2 under chronic stress, loss of ACTN2 function accelerated H9c2 hypertrophy through ERK signaling. A commercial drug, Ibudilast, was identified to reverse cell hypertrophy in vitro.</p>","PeriodicalId":12675,"journal":{"name":"Genes & genomics","volume":null,"pages":null},"PeriodicalIF":1.6,"publicationDate":"2024-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141579455","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":"Discovery of high-expressing lncRNA-derived sORFs as potential tumor-associated antigens in hepatocellular carcinoma.","authors":"Yooeun Kim, Hongseok Ha, Kwangsoo Kim","doi":"10.1007/s13258-024-01549-z","DOIUrl":"10.1007/s13258-024-01549-z","url":null,"abstract":"<p><strong>Background: </strong>This study is based on deep mining of Ribo-seq data for the identification of lncRNAs that have highly expressed sORFs in HCC. In this paper, dynamic prospects associated with sORFs acting as newly defined tumor-specific epitopes are discussed with possible improvement in strategies for tumor immunotherapy.</p><p><strong>Objective: </strong>Using ribosome profiling to identify and characterize sORFs within lncRNAs in HCC, identify potential therapeutic targets and tumor-specific epitopes applicable for immunotherapy.</p><p><strong>Methods: </strong>MetamORF performed the identification of sORFs with deep analysis of the data of ribosome profiling in lncRNAs associated with HCC. The translation efficiency in these molecules was estimated, and epitope prediction was done by pVACbind. Peptide search was done to check the presence of micropeptides translated from these identified sORFs. validated translational activity and identified potential epitopes.</p><p><strong>Results: </strong>Higher translation efficiency was noted in the case of lncRNAs associated with HCC compared to normal tissues. Of particular note is ORF3418981, which results in the highest expression and has supporting experimental evidence at the protein level. Epitope prediction identified a putative epitope at the C-terminus of ORF3418981.</p><p><strong>Conclusions: </strong>This study uncovers the as-yet-unknown potential of lncRNA-derived sORFs as sources of tumor antigens, shifting the research focus from protein-coding genes to non-coding RNAs also in the HCC context. Moreover, this study highlights the contribution of a subset of lncRNAs, especially LINC00152, to the development of tumors and modulation of the immune response by its sORFs.</p>","PeriodicalId":12675,"journal":{"name":"Genes & genomics","volume":null,"pages":null},"PeriodicalIF":1.6,"publicationDate":"2024-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141901447","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":"Genome-wide identification of cold shock proteins (CSPs) in sweet cherry (Prunus avium L.) and exploring the differential responses of PavCSP1 and PavCSP3 to low temperature and salt stress.","authors":"Pan Guo, Ao Liu, Yueting Qi, Xueting Wang, Xiaole Fan, Xiaotong Guo, Chunyan Yu, Changping Tian","doi":"10.1007/s13258-024-01542-6","DOIUrl":"10.1007/s13258-024-01542-6","url":null,"abstract":"<p><strong>Background: </strong>Cold shock proteins (CSPs) are ubiquitous nucleic acid-binding proteins involved in growth, development, and stress response across various organisms. While extensively studied in many species, their regulatory roles in sweet cherry (Prunus avium L.) remain unclear.</p><p><strong>Objective: </strong>To identify and analyze CSP genes (PavCSPs) in sweet cherry genome, and explore the differential responses of PavCSP1 and PavCSP3 to low temperature and salt stress.</p><p><strong>Methods: </strong>Three methods were employed to identify and characterize CSP in sweet cherry genomes. To explore the potential functions and evolutionary relationships of sweet cherry CSP proteins, sequence alignment and phylogenetic tree incorporating genes from five species were conducted and constructed, respectively. To investigate the responses to abiotic stresses, cis-acting elements analysis and gene expression patterns to low-temperature and salt stress were examined. Moreover, transgenic yeasts overexpressing PavCSP1 or PavCSP3 were generated and their growth under stress conditions were observed.</p><p><strong>Results: </strong>In this study, three CSP genes (PavCSPs) were identified and comprehensively analyzed. The quantitative real-time PCR revealed diverse expression patterns, with PavCSP1-3 demonstrating a particular activity in the upper stem and all members were responsive to low-temperature and salt stress. Further investigation demonstrated that transgenic yeasts overexpressing PavCSP1 or PavCSP3 exhibited improved growth states following high-salt and low-temperature stress.</p><p><strong>Conclusion: </strong>These findings elucidated the responses of PavCSP1 and PavCSP3 to salt and low-temperature stresses, laying the groundwork for further functional studies of PavCSPs in response to abiotic stresses.</p>","PeriodicalId":12675,"journal":{"name":"Genes & genomics","volume":null,"pages":null},"PeriodicalIF":1.6,"publicationDate":"2024-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141599101","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":"Genomic analyses of intricate interaction of TE-lncRNA overlapping genes with miRNAs in human diseases.","authors":"Du Hyeong Lee, Eun Gyung Park, Jung-Min Kim, Hae Jin Shin, Yun Ju Lee, Hyeon-Su Jeong, Hyun-Young Roh, Woo Ryung Kim, Hongseok Ha, Sang-Woo Kim, Yung Hyun Choi, Heui-Soo Kim","doi":"10.1007/s13258-024-01547-1","DOIUrl":"https://doi.org/10.1007/s13258-024-01547-1","url":null,"abstract":"<p><strong>Background: </strong>Transposable elements (TEs) are known to be inserted into genome to create transcript isoforms or to generate long non-coding RNA (lncRNA) sequences. The insertion of TEs generates a gene protein sequence within the genome, but also provides a microRNA (miRNA) regulatory region.</p><p><strong>Objective: </strong>To determine the effect of gene sequence changes caused by TE insertion on miRNA binding and to investigate the formation of an overlapping lncRNA that represses it.</p><p><strong>Methods: </strong>The distribution of overlapping regions between exons and TE regions with lncRNA was examined using the Bedtools. miRNAs that can bind to those overlapping regions were identified through the miRDB web program. For TE-lncRNA overlapping genes, bioinformatic analysis was conducted using DAVID web database. Differential expression analysis was conducted using data from the GEO dataset and TCGA.</p><p><strong>Results: </strong>Most TEs were distributed more frequently in untranslated regions than open reading frames. There were 30 annotated TE-lncRNA overlapping genes with same strand that could bind to the same miRNA. As a result of identifying the association between these 30 genes and diseases, TGFB2, FCGR2A, DCTN5, and IFI6 were associated with breast cancer, and HMGCS1, FRMD4A, EDNRB, and SNCA were associated with Alzheimer's disease. Analysis of the GEO and TCGA data showed that the relevant expression of miR-891a and miR-28, which bind to the TE overlapping region of DCTN5 and HMGCS1, decreased.</p><p><strong>Conclusion: </strong>This study indicates that the interaction between TE-lncRNA overlapping genes and miRNAs can affect disease progression.</p>","PeriodicalId":12675,"journal":{"name":"Genes & genomics","volume":null,"pages":null},"PeriodicalIF":1.6,"publicationDate":"2024-08-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142106599","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":"Transcriptome analysis of East Asian common octopus, Octopus sinensis, paralarvae.","authors":"Ki Tae Kim, Mi Ae Kim, Woo Jin Kim, Min Min Jung, Dong Hwi Kim, Young Chang Sohn","doi":"10.1007/s13258-024-01537-3","DOIUrl":"10.1007/s13258-024-01537-3","url":null,"abstract":"<p><strong>Background: </strong>The genes involved in cephalopod development and their association with hatching and survival during early life stages have been extensively studied. However, few studies have investigated the paralarvae transcriptome of the East Asian common octopus (Octopus sinen sis).</p><p><strong>Objective: </strong>This study aimed to identify the genes related to embryonic development and hatching in O. sinensis using RNA sequencing (RNA-seq) and verify the genes most relevant to different embryonic stages.</p><p><strong>Methods: </strong>RNA samples from hatched and 25 days post-hatching (dph) O. sinensis paralarvae were used to construct cDNA libraries. Clean reads from individual samples were aligned to the reference O. sinensis database to identify the differentially expressed genes (DEGs) between the 0- and 25-dph paralarvae libraries. Real-time quantitative polymerase chain reaction (RT-qPCR) was used to supplement the RNA-seq data for embryogenic developmental stages.</p><p><strong>Results: </strong>A total of 12,597 transcripts were annotated and 5,468 DEGs were identified between the 0- and 25-dph O. sinensis paralarvae, including 2,715 upregulated and 2,753 downregulated transcripts in the 25-dph paralarvae. Several key DEGs were related to transmembrane transport, lipid biosynthesis, monooxygenase activity, lipid transport, neuropeptide signaling, transcription regulation, and protein-cysteine S-palmitoyltransferase activity during the post-hatching development of O. sinensis paralarvae. RT-qPCR analysis further revealed that SLC5A3A, ABCC12, and NPC1 transcripts in 20 and/or 30 days post-fertilization (dpf) embryos were significantly higher (p < 0.05) than those in 10-dpf embryos.</p><p><strong>Conclusion: </strong>Transcriptome profiles provide molecular targets to understand the embryonic development, hatching, and survival of O. sinensis paralarvae, and enhance octopus production.</p>","PeriodicalId":12675,"journal":{"name":"Genes & genomics","volume":null,"pages":null},"PeriodicalIF":1.6,"publicationDate":"2024-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141450312","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":"Four mutations identified in Chinese families with autosomal dominant congenital cataracts by next-generation sequencing.","authors":"Xinyi Yang, Zitong Zhao, Chun Wang, Wenxuan Wang, Lu Zhang","doi":"10.1007/s13258-024-01525-7","DOIUrl":"10.1007/s13258-024-01525-7","url":null,"abstract":"<p><strong>Background: </strong>Congenital cataracts, which can arise due to a combination of factors like environmental influences and genetic predisposition, significantly impact children's visual health globally. The occurrence rate of congenital cataracts varies from 0. 63 to 9.74 per 10,000 births. There are 7.4 instances per 10,000 children, with the highest occurrence seen in Asia. Symptoms of the disease include clouding of the lens and visual impairment. Timely identification of the condition plays a crucial role in the management and outlook of pediatric patients.</p><p><strong>Objective: </strong>This investigation aimed to discover causative mutations in four separate Chinese family lineages.</p><p><strong>Methods: </strong>The detailed clinical data and family history of four Chinese families with autosomal dominant congenital cataracts were carefully documented. Examination of the Whole Exome Sequencing was utilized to identify the genetic anomalies present in the familial cases. Subsequent validation of the identified mutations was carried out using PCR and Sanger sequencing. Following this, various computational predictive programs were utilized to evaluate how the mutations impact the structure and function of the protein.</p><p><strong>Results: </strong>The sequencing results reveal four potential disease-causing mutations: c.436G > A (p.V146M) of CRYBB2 Family 1, c.26G > T (p.R9I) of GJA3 in family 2, c.227G > A (p.R76H) of GJA8 in family 3, c.-168G > T of FTL in family 4. Among them, the causative mutation in Family GJA3 is novel, and Family FTL is a rare cataract syndrome. These familial mutations showed complete co-segregation with the affected individuals, with no presence in unaffected family members or the 100 controls. Several bioinformatic prediction tools also support the likely pathogenicity of these mutations.</p><p><strong>Conclusion: </strong>Our findings expand the mutational and phenotypic spectrum of genes associated with congenital cataracts and provide clues to the pathogenesis of congenital cataracts. These data also demonstrate the importance of NGS technology for the molecular diagnosis of congenital cataract patients.</p>","PeriodicalId":12675,"journal":{"name":"Genes & genomics","volume":null,"pages":null},"PeriodicalIF":1.6,"publicationDate":"2024-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141310518","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":"Genomic analysis uncovers that cold-inducible RNA binding protein is associated with estrogen receptor in breast cancer.","authors":"Eun-Yeung Gong, Dana Jung, Hyunmin Woo, Jinhoo Song, Eunjeong Choi, Seo-Gyeong Jo, Seong-Il Eyun, Seokho Kim, Yun-Yong Park","doi":"10.1007/s13258-024-01530-w","DOIUrl":"10.1007/s13258-024-01530-w","url":null,"abstract":"<p><strong>Background: </strong>RNA-binding proteins (RBPs) perform various biological functions in humans and are associated with several diseases, including cancer. Therefore, RBPs have emerged as novel therapeutic targets. Although recent investigations have shown that RBPs have crucial functions in breast cancer (BC), detailed research is underway to determine the RBPs that are closely related to cancers.</p><p><strong>Objective: </strong>To provide an insight into estrogen receptor (ER) regulation by cold-inducible RNA binding protein (CIRBP) as a novel therapeutic target.</p><p><strong>Results: </strong>By analyzing the genomic data, we identified a potential RBP in BC. We found that CIRBP is highly correlated with ER function and influences clinical outcomes, such as patient survival and endocrine therapy responsiveness. In addition, CIRBP influences the proliferation of BC cells by directly binding to ER-RNA.</p><p><strong>Conclusion: </strong>Our results suggest that CIRBP is a novel upstream regulator of ER and that the interplay between CIRBP and ER may be associated with the clinical relevance of BC.</p>","PeriodicalId":12675,"journal":{"name":"Genes & genomics","volume":null,"pages":null},"PeriodicalIF":1.6,"publicationDate":"2024-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141283485","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":"A novel role of the cotton calcium sensor CBL3 was involved in Verticillium wilt resistance in cotton.","authors":"Shengqi Gao, Xiaoyan Hao, Guo Chen, Wenran Hu, Zhun Zhao, Wukui Shao, Jianping Li, Quansheng Huang","doi":"10.1007/s13258-024-01528-4","DOIUrl":"10.1007/s13258-024-01528-4","url":null,"abstract":"<p><strong>Background: </strong>Verticillium wilt, causes mainly by the soilborne pathogen Verticillium dahliae, is a devastated vascular disease resulting in huge financial losses in cotton, so research on improving V. dahliae stress tolerance in cotton is the utmost importance. Calcium as the second messenger acts as a crucial role in plant innate immunity. Cytosolic Ca²⁺during the pathogen infection is a significant increase in plant immune responses. Calcineurin B-like (CBL) proteins are widely known calcium sensors that regulate abiotic stress responses. However, the role of cotton CBLs in response to V. dahliae stress remains unclear.</p><p><strong>Objective: </strong>To discover and utilize the gene to Verticillium wilt resistance and defense response mechanism of cotton.</p><p><strong>Methods: </strong>Through screening the gene to Verticillium wilt resistance in cotton, four GhCBL3 copies were obtained from the current common cotton genome sequences. The protein domain and phylogenetic analyses of GhCBL3 were performed using NCBI Blast, DNAMAN, and MotifScan programs. Real-time RT-PCR was used to detect the expression of GhCBL3 gene in cotton seedlings under various stress treatments. The expression construct including GhCBL3 cDNA was transduced into Agrobacterium tumefaciens (GV3101) by heat shock method and transformed into cotton plants by Virus-Induced Gene Silencing (VIGS) method. The results of silencing of GhCBl3 on ROS accumulation and plant disease resistance in cotton plants were assessed.</p><p><strong>Results: </strong>A member of calcineurin B-like proteins (defined as GhCBL3) in cotton was obtained. The expression of GhCBL3 was significantly induced and raised by various stressors, including dahliae, jasmonic acid (JA) and H₂O₂ stresses. Knockdown GhCBL3 in cotton by Virus-Induced Gene Silencing analysis enhanced Verticillium wilt tolerance and changed the occurrence of reactive oxygen species. Some disease-resistant genes were increased in GhCBL3-silencing cotton lines.</p><p><strong>Conclusion: </strong>GhCBL3 may function on regulating the Verticillium dahliae stress response of plants.</p>","PeriodicalId":12675,"journal":{"name":"Genes & genomics","volume":null,"pages":null},"PeriodicalIF":1.6,"publicationDate":"2024-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141327424","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}