Functional & Integrative Genomics最新文献

{"title":"Impact of structural variations and genome partitioning on bread wheat hybrid performance","authors":"Kevin Gimenez,&nbsp;Pierre Blanc,&nbsp;Odile Argillier,&nbsp;Jonathan Kitt,&nbsp;Jean-Baptiste Pierre,&nbsp;Jacques Le Gouis,&nbsp;Etienne Paux","doi":"10.1007/s10142-024-01512-x","DOIUrl":"10.1007/s10142-024-01512-x","url":null,"abstract":"<div><p>The agronomical interest of hybrid wheat has long been a matter of debate. Compared to maize where hybrids have been successfully grown for decades, the mixed results obtained in wheat have been attributed at least partially to the lack of heterotic groups. The wheat genome is known to be strongly partitioned and characterized by numerous presence/absence variations and alien introgressions which have not been thoroughly considered in hybrid breeding. The objective was to investigate the relationships between hybrid performance and genomic diversity. For this, we characterized a set of 124 hybrids as well as their 19 female and 16 male parents. Phenotyping for yield and yield components was conducted during two years in three locations. Parental lines were genotyped using a 410 K SNP array as well as through sequence capture of roughly 200,000 loci. This led to the identification of 180 structural variations including presence-absence variations and alien introgressions. Twenty-six of them were associated to hybrid performance through either additivity or dominance effects. While no correlation was observed at the whole genome level, the genetic distance for 25 genomic regions resulting from the structural and functional partitioning of the chromosomes shown positive or negative correlation with agronomic traits including yield. Large introgressions, like the <i>Aegilops ventricosa</i> 2NS-2AS translocation, can correspond to entire chromosomal regions, such as the R1 region, with an impact on yield. Our results suggest hybrid breeding should consider both structural variations and chromosome partitioning rather than maximizing whole-genome genetic distance, and according to genomic regions to combine homozygosity and heterozygosity.</p></div>","PeriodicalId":574,"journal":{"name":"Functional & Integrative Genomics","volume":"25 1","pages":""},"PeriodicalIF":3.9,"publicationDate":"2025-01-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142938731","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":"Epigenetic modification mediated by PHF20/METTL14/HOXA13 signaling axis modulates osteogenic differentiation of mesenchymal stem cells","authors":"Weijia Feng,&nbsp;Ting Chen","doi":"10.1007/s10142-024-01516-7","DOIUrl":"10.1007/s10142-024-01516-7","url":null,"abstract":"<div><p>This study investigates the mechanism of PHF20 in osteogenic differentiation of bone marrow mesenchymal stem cells (BMSCs). BMSCs from Balb/c mouse were cultured and identified through osteogenesis, adipogenesis, and flow cytometry. After osteogenic induction, the levels of OPN and OCN in BMSCs were detected by RT-qPCR. Alizarin red staining and alkaline phosphatase (ALP) staining were used to evaluate the osteogenic differentiation ability of BMSCs. PHF20, METTL14, and HOXA13 expressions were detected by RT-qPCR and Western blot. After quantitative analysis of m6A level, RNA immunoprecipitation (RIP) was performed to measure the enrichment of IGF2BP3 or m6A on HOXA13 mRNA. HOXA13 mRNA stability was assessed after actinomycin D treatment. PHF20, METT14, and HOXA13 expressions gradually increased during osteogenic differentiation of BMSCs. Suppression of PHF20 expression repressed the osteogenic differentiation of BMSCs, mainly resulted in a decrease in OPN and OCN levels, reduced mineralization, and weakened ALP activity. Mechanistically, PHF20 elevated METTL14 expression by enhancing the enrichment of H3K4me3 on its promoter, and METTL14 strengthened HOXA13 m6A methylation to maintain HOXA13 mRNA stability through IGF2BP3. In conclusion, PHF20 elevates METTL14 expression by enhancing H3K4me3 enrichment on its promoter and enhances HOXA13 mRNA stability via IGF2BP3-mediated m6A modification, thus facilitating HOXA13 expression and eventually inducing osteogenic differentiation of BMSCs.</p></div>","PeriodicalId":574,"journal":{"name":"Functional & Integrative Genomics","volume":"25 1","pages":""},"PeriodicalIF":3.9,"publicationDate":"2025-01-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142925600","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":"Application of a high-throughput swarm-based deep neural network Algorithm reveals SPAG5 downregulation as a potential therapeutic target in adult AML","authors":"Chinyere I Ajonu,&nbsp;Robert I Grundy,&nbsp;Graham R Ball,&nbsp;Dimitrios Zafeiris","doi":"10.1007/s10142-024-01514-9","DOIUrl":"10.1007/s10142-024-01514-9","url":null,"abstract":"<div><p>Gene‒gene interactions play pivotal roles in disease pathogenesis and are fundamental in the development of targeted therapeutics, particularly through the elucidation of oncogenic gene drivers in cancer. The systematic analysis of pathways and gene interactions is critical in the drug discovery process for various cancer subtypes. SPAG5, known for its role in spindle formation during cell division, has been identified as an oncogene in several cancers, although its specific impact on AML remains underexplored. This study leverages a high-throughput swarm-based deep neural network (SDNN) and transcriptomic data—an approach that enhances predictive accuracy and robustness through collective intelligence—to augment, model, and enhance the understanding of the TP53 pathway in AML cohorts. Our integrative systems biology approach identified SPAG5 as a uniquely downregulated driver in adult AML, underscoring its potential as a novel therapeutic target. The interaction of SPAG5 with key hub genes such as MDM2 and CDK1 not only reinforces its role in tumour suppression through negative regulation but also highlights its potential in moderating the phenotypic and genomic alterations associated with AML progression. This study of the role and interaction dynamics of SPAG5 sets the stage for future research aimed at developing targeted and personalized treatment approaches for AML, utilizing the capabilities of genetic interventions.</p></div>","PeriodicalId":574,"journal":{"name":"Functional & Integrative Genomics","volume":"25 1","pages":""},"PeriodicalIF":3.9,"publicationDate":"2025-01-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s10142-024-01514-9.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142938931","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":"A cutting-edge investigation of the multifaceted role of SOX family genes in cancer pathogenesis through the modulation of various signaling pathways","authors":"Saade Abdalkareem Jasim,&nbsp;Shireen Hamid Farhan,&nbsp;Irfan Ahmad,&nbsp;Ahmed Hjazi,&nbsp;Ashwani Kumar,&nbsp;Mohammed Abed Jawad,&nbsp;Atreyi Pramanik,&nbsp;M. A. Farag Altalbawy,&nbsp;Salim B. Alsaadi,&nbsp;Munther Kadhim Abosaoda","doi":"10.1007/s10142-024-01517-6","DOIUrl":"10.1007/s10142-024-01517-6","url":null,"abstract":"<div><p>This detailed study examines the complex role of the SOX family in various tumorigenic contexts, offering insights into how these transcription factors function in cancer. As the study progresses, it explores the specific contributions of each SOX family member. The significant roles of the SOX family in the oncogenic environment are well-recognized, highlighting a range of regulatory mechanisms that influence tumor progression. In brain, lung, and colorectal cancers, SOX types like SOX2, SOX3, and SOX4 promote the migration, proliferation, and angiogenesis of cancer cells. Conversely, in pancreatic, gastric, and breast cancers, SOX types, including SOX1, SOX9, and SOX17 inhibit various cancer cell activities such as proliferation and invasion. This thorough investigation enhances our understanding of the SOX family’s complex role in cancer, establishing a foundation for future research and potential therapeutic strategies targeting these versatile transcription factors.</p></div>","PeriodicalId":574,"journal":{"name":"Functional & Integrative Genomics","volume":"25 1","pages":""},"PeriodicalIF":3.9,"publicationDate":"2025-01-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142925589","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":"Towards assembling functional cyanobacterial β-carboxysomes in Oryza sativa chloroplasts","authors":"Gurbir Kaur Sidhu,&nbsp;Rakesh Pandey,&nbsp;Gurdeep Kaur,&nbsp;Anjulata Singh,&nbsp;Sangram K. Lenka,&nbsp;Pallavolu M. Reddy","doi":"10.1007/s10142-024-01518-5","DOIUrl":"10.1007/s10142-024-01518-5","url":null,"abstract":"<div><p>The major limiting factor of photosynthesis in C3 plants is the enzyme, rubisco which inadequately distinguishes between carbon dioxide and oxygen. To overcome catalytic deficiencies of Rubisco, cyanobacteria utilize advanced protein microcompartments, called the carboxysomes which envelopes the enzymes, Rubisco and Carbonic Anhydrase (CA). These microcompartments facilitate the diffusion of bicarbonate ions which are converted to CO₂ by CA, following in an increase in carbon flux near Rubisco boosting CO₂ fixation process. Inspired by this mechanism, our study aims to improve photosynthetic efficiency in the C₃ model crop, rice (<i>Oryza sativa</i>), by stably engineering the genetic components of the β-carboxysome of <i>Synechococcus elongatus</i> PCC 7942 (hereafter, Syn7942) in the rice genome. We demonstrated this proof of concept by developing two types of transgenic rice plants. The first type involved targeting the chloroplasts with three key carboxysome structural proteins (<i>ccmL</i>, <i>ccmO</i>, and <i>ccmK</i>) and a chimeric protein (<i>ccmC</i>), which integrates domains from four distinct carboxysome proteins. The second type combined these proteins with the introduction of cyanobacterial Rubisco targeted to chloroplasts. Additionally, in the second transgenic background, RNA interference was employed to silence the endogenous rice Rubisco along with stromal carbonic anhydrase gene. The transgenic plants exhibited the assembly of carboxysome-like compartments and aggregated proteins in the chloroplasts and the second type demonstrated reduced plant growth and yield. We have followed a bottom-up approach for targeting the cyanobacterial CCM in rice chloroplast which would help in stacking up the components further required for increasing the photosynthetic efficiency in future.</p></div>","PeriodicalId":574,"journal":{"name":"Functional & Integrative Genomics","volume":"25 1","pages":""},"PeriodicalIF":3.9,"publicationDate":"2025-01-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142912916","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":"Circular RNAs in the pathogenesis of SARS-CoV-2: potential diagnostic biomarkers and therapeutic targets","authors":"JiaJie Wu,&nbsp;Lele Li,&nbsp;Wei Xu,&nbsp;Xiaoping Xia,&nbsp;Yingping Wu","doi":"10.1007/s10142-024-01509-6","DOIUrl":"10.1007/s10142-024-01509-6","url":null,"abstract":"<div><p>Since December 2019, the global dissemination of a novel coronavirus has precipitated a notable public health crisis, prompting considerable interest and scrutiny from governmental and scholarly entities. Substantial research efforts have been dedicated to exploring diverse facets of this novel coronavirus, encompassing its pathogenesis, transmission dynamics, and therapeutic interventions. Recent findings suggest that circular RNAs (circRNAs) exert a pivotal influence on modulating viral infectivity and immune defense mechanisms. The detection of differentially expressed circRNAs in individuals afflicted with SARS-CoV-2 signifies a noteworthy advancement in understanding the molecular mechanisms underpinning viral pathogenesis.</p></div>","PeriodicalId":574,"journal":{"name":"Functional & Integrative Genomics","volume":"25 1","pages":""},"PeriodicalIF":3.9,"publicationDate":"2025-01-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142912999","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":"Unraveling the organellar genomic landscape of the therapeutic and entheogenic plant Mimosa tenuiflora: insights into genetic, structural, and evolutionary dynamics","authors":"Vitor Trinca,&nbsp;Saura R. Silva,&nbsp;João V. A. Almeida,&nbsp;Vitor F. O. Miranda,&nbsp;José V. Costa-Macedo,&nbsp;Tatiane K. B. A. Carnaval,&nbsp;Draulio B. Araújo,&nbsp;Francisco Prosdocimi,&nbsp;Alessandro M. Varani","doi":"10.1007/s10142-024-01511-y","DOIUrl":"10.1007/s10142-024-01511-y","url":null,"abstract":"<div><p><i>Mimosa tenuiflora</i>, popularly known as “Jurema-Preta”, is a perennial tree or shrub native to the tropical regions of the Americas, particularly among Afro-Brazilian and Indigenous Brazilian communities. Known for producing N,N-Dimethyltryptamine, a psychedelic compound with profound psychological effects, Jurema-Preta has been studied for its therapeutic potential in mental health. This study offers a comprehensive analysis of the plastid (ptDNA) and mitochondrion (mtDNA) genomes of <i>M. tenuiflora</i>. The 165,639 bp ptDNA sequence features the classical quadripartite structure with 130 protein-coding genes. Comparative genomics among <i>Mimosa</i> species shows high sequence identity in protein-coding genes, with variation in the <i>rpoC1</i>, <i>clpP</i>, <i>ndhA</i>, and <i>ycf1</i> genes. The ptDNA junctions display distinct features, such as the deletion of the <i>rpl22</i> gene, and specific simple sequence repeats highlight genetic variation and unique motifs as valuable genetic markers for population studies. Phylogenetic analysis places <i>M. tenuiflora</i> in the Caesalpinioideae, closely related to <i>M. pigra</i> and <i>M. pudica</i>. The 617,839 bp mtDNA sequence exhibits a complex structure with multiple genomic arrangements due to large repeats, encoding 107 protein-coding genes, including the ptDNA <i>petG</i> and <i>psaA</i> genes, and non-retroviral RNA mitoviruses sequences. Comparative analysis across Fabaceae species reveals limited conservation, emphasizing the dynamic nature of plant mitochondrial genomes. The genomic characterization of <i>M. tenuiflora</i> enhances understanding of its evolutionary dynamics, providing insights for population studies and potential applications in ethnopharmacology and conservation.</p></div>","PeriodicalId":574,"journal":{"name":"Functional & Integrative Genomics","volume":"25 1","pages":""},"PeriodicalIF":3.9,"publicationDate":"2024-12-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142905987","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":"Barley stripe mosaic virus-induced gene silencing for functional validation of abiotic stress in barley","authors":"Tayachew Admas,&nbsp;Maru Wudu,&nbsp;Hailu Berhanie","doi":"10.1007/s10142-024-01508-7","DOIUrl":"10.1007/s10142-024-01508-7","url":null,"abstract":"<div><p>The <i>barley stripe mosaic virus</i> (<i>BSMV</i>) uses its genomic RNA components (alpha, beta, and gamma) as an efficient method for studying gene functions. It is a newly developed method that utilizes gene transcript suppression to determine the role of plant genes. <i>BSMV</i> derived from virus induced gene silencing (VIGS) is capable of infecting various key farming crops like barley, wheat, rice, corn, and oats. Nevertheless, the growing acceptance and enhancement of <i>BSMV</i>-VIGS will benefit all kinds of plants. Abiotic stresses such as drought and salt are highly affecting plant growth, development, and production. <i>BSMV</i>-induced temporal gene knockdown is performed during particular stressful situations to determine their specific function. The quick physiological and biochemical changes aid in confirming the role of the target genes. VIGS has a significant role to improve crop genetics and breeding, despite having certain restrictions. Thus, exploring the possible solution and addressing these difficulties will enhance the technology in the continuous advancement of plant manufacturing. <i>BSMV</i>-mediated VIGS has become popular in functional genomics; gene function can be determined without permanent transformation. In general, <i>BSMV</i>-mediated VIGS will be very helpful in the ongoing effort to develop resilient crops.</p></div>","PeriodicalId":574,"journal":{"name":"Functional & Integrative Genomics","volume":"25 1","pages":""},"PeriodicalIF":3.9,"publicationDate":"2024-12-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142889562","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":"Xuanhong Dingchuan Tang suppresses bronchial asthma inflammation via the microRNA-107-3p/PTGS2/MAPK axis","authors":"Xi Ming,&nbsp;Yingzhu Lu,&nbsp;Huihui Huang,&nbsp;Jialin Zheng,&nbsp;Tianzi Wang,&nbsp;Zhuoqun Li,&nbsp;Xingzhu Yu,&nbsp;Lei Xiong","doi":"10.1007/s10142-024-01506-9","DOIUrl":"10.1007/s10142-024-01506-9","url":null,"abstract":"<div><p>This study aimed to investigate the mechanism of Xuanhong Dingchuan Tang (XHDCT) in delaying bronchial asthma inflammation via the microRNA (miR)-107-3p/prostaglandin endoperoxide synthase 2 (PTGS2)/mitogen-activated protein kinase (MAPK) axis. Based on the network pharmacological analysis, XHDCT chemical constituents and targets of each chemical constituent were screened through the TCMSP database, and differential-expressed genes of bronchial asthma were obtained from the GEO database, which were intersected to get XHDCT potential anti-inflammatory targets. The key anti-inflammatory targets of XHDCT were acquired by protein-protein interaction (PPI) analysis of the candidate targets. Bronchial asthma mouse models were established and the pathological changes of lung tissues were observed. Serum IgE levels were tested. Total cells and eosinophils in bronchoalveolar lavage fluid (BALF) were counted. The expression of Th2-associated cytokines (interleukin (IL)-4, IL-5, and IL-13) and chemokines (monocyte chemoattractant protein-1 (MCP-1) and eotaxin) in BALF were measured. The targeting relationship between miR-107-3p and PTGS2 was tested. XHDCT delayed bronchial asthma inflammation in in-vivo asthma mouse models. A total of 155 active ingredients and their 341 targets were intersected with bronchial asthma-relevant genes, obtaining 20 potential targets of XHDCT for bronchial asthma treatment. Based on the PPI and “drug-component-target” network diagram, PTGS2 was found to be in a central position. PTGS2 was downregulated and miR-107-3p was upregulated in bronchial asthma mice after XHDCT treatment. PTGS2 overexpression activated the MAPK signaling pathway to promote inflammation in bronchial asthma mice, whereas inflammatory symptoms were reduced and the MAPK signaling pathway was inhibited after XHDCT treatment. miR-107-3p was an upstream regulatory miRNA for PTGS2. After miR-107-3p interference, the activation of the PTGS2/MAPK axis promoted inflammation in bronchial asthma mice, whereas the inflammatory symptoms were reduced after XHDCT treatment. XHDCT promotes anti-inflammatory effects in bronchial asthma via the miR-107-3p/PTGS2/MAPK axis.</p></div>","PeriodicalId":574,"journal":{"name":"Functional & Integrative Genomics","volume":"25 1","pages":""},"PeriodicalIF":3.9,"publicationDate":"2024-12-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142859698","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":"Correction to: Decoding the role of durum wheat ascorbate peroxidase TdAPX7B-2 in abiotic stress response","authors":"Kaouthar Feki,&nbsp;Sana Tounsi,&nbsp;Hanen Kamoun,&nbsp;Abdulrahman Al-Hashimi,&nbsp;Faiçal Brini","doi":"10.1007/s10142-024-01507-8","DOIUrl":"10.1007/s10142-024-01507-8","url":null,"abstract":"","PeriodicalId":574,"journal":{"name":"Functional & Integrative Genomics","volume":"24 6","pages":""},"PeriodicalIF":3.9,"publicationDate":"2024-12-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142810846","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}