Functional & Integrative Genomics最新文献

{"title":"Andrographis restrains the progression of colorectal cancer by inhibiting the KLF3/LEMD1 axis","authors":"Leyi Zhang,&nbsp;Dongyang Li,&nbsp;Yan Tang,&nbsp;Yicheng Xie","doi":"10.1007/s10142-026-01877-1","DOIUrl":"10.1007/s10142-026-01877-1","url":null,"abstract":"<div><p>Andrographis has anti-cancer activity in various human cancers, including colorectal cancer. Our aim was to explore the detailed mechanisms underlying Andrographis in colorectal cancer progression. Andrographis inhibited the proliferation, reduced the invasive ability, and induced apoptosis in LoVo and HCT-116 cells. LEM domain containing 1 (LEMD1) expression was upregulated in colorectal cancer cells and tissue samples, and Andrographis significantly decreased LEMD1 expression in LoVo and HCT-116 cells. LEMD1 knockdown restrained colorectal cancer development by inhibiting proliferation and invasion and triggering apoptosis. Krüppel-like factor 3 (KLF3) targeted LEMD1 and positively regulated its expression in colorectal cancer cells. KLF3 overexpression reversed the anti-tumor effects of Andrographis on LoVo and HCT-116 cells, and this reversal was attenuated by LEMD1 silencing. Additionally, Andrographis hampered tumor growth and downregulated KLF3 and LEMD1 expression in colorectal cancer mice. In conclusion, Andrographis exerts anti-tumor activity in colorectal cancer through decreasing KLF3 and LEMD1 expression.</p></div>","PeriodicalId":574,"journal":{"name":"Functional & Integrative Genomics","volume":"26 1","pages":""},"PeriodicalIF":3.1,"publicationDate":"2026-05-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147829973","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 and metabolomic characterization of Acinetobacter calcoaceticus (DT1) and Citrobacter braakii (S10) reveal functional traits for plant stress alleviation and sustainable agriculture","authors":"Imen Ghazala,&nbsp;Naïma Sayahi,&nbsp;Abdelmalek Alioua,&nbsp;Valérie Cognat,&nbsp;Dimitri Heintz,&nbsp;Claire Villette,&nbsp;Julie Zumsteg,&nbsp;Moez Hanin,&nbsp;Alexandre Berr,&nbsp;Chantal Ebel","doi":"10.1007/s10142-026-01879-z","DOIUrl":"10.1007/s10142-026-01879-z","url":null,"abstract":"<div><p>Plant growth-promoting rhizobacteria (PGPR) enhance plant growth and development through diverse mechanisms, including phytohormone production, nutrient acquisition, and stress mitigation. This study describes the isolation and characterization of two bacterial strains, DT1 and S10, from the rhizospheres of <i>Diplotaxis tenuifolia</i> and <i>Cynodon dactylon</i>, respectively that exhibit multiple plant growth‑promoting traits, including phosphate and zinc solubilization, nitrogen metabolism and the production of indole acetic acid (IAA) and siderophores. Using whole genome sequencing and taxonomic analyses, these two strains were identified as <i>Acinetobacter calcoaceticus</i> (DT1) and <i>Citrobacter braakii</i> (S10). Functional genomic annotation revealed numerous genes associated with key plant growth-promoting traits, including those involved in indole-3-acetic acid (IAA) (<i>trp</i>ABCDE, <i>ipd</i>C), cytokinin (<i>miaABE</i>), and riboflavin biosynthesis, which were further supported by targeted metabolomic analyses. In addition, genes associated with nitrogen metabolism, including nitrate/nitrite reduction (<i>nir</i>B, <i>nar</i>GHI), as well as phosphate solubilization (<i>gcd</i>, <i>pho</i>ARP, <i>pst</i>ABCS, <i>pqq</i>EFG) were identified and supported by phenotypic assays. Interestingly, biosynthetic gene clusters for the secondary metabolites enterobactin, bacillibactin, and staphyloferrin B, known to contribute to plant growth promotion, were identified in both genomes. Both strains also harbored genes potentially involved in stress-related metabolic processes. Furthermore, non-targeted metabolomic analysis revealed that DT1 and S10 produced a range of intracellular and extracellular metabolites associated with plant growth promotion and stress resilience, including cadaverine, biotin, arginine, and GABA. Collectively, these findings position DT1 and S10 as promising bioinoculant candidates, offering an integrative genomic and metabolic foundation for their application in next-generation sustainable agricultural strategies.</p></div>","PeriodicalId":574,"journal":{"name":"Functional & Integrative Genomics","volume":"26 1","pages":""},"PeriodicalIF":3.1,"publicationDate":"2026-05-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147829980","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: Transcription factor LchiTCP1 modulates abiotic stress response in Arabidopsis","authors":"Hwarari Delight,&nbsp;Yinyue Zuo,&nbsp;Yao Zhang,&nbsp;Xinyi Cao,&nbsp;Tian Min,&nbsp;Jinhui Chen,&nbsp;Liming Yang","doi":"10.1007/s10142-026-01876-2","DOIUrl":"10.1007/s10142-026-01876-2","url":null,"abstract":"","PeriodicalId":574,"journal":{"name":"Functional & Integrative Genomics","volume":"26 1","pages":""},"PeriodicalIF":3.1,"publicationDate":"2026-05-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147829781","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":"Comparative mitochondrial genome architecture and nuclear mitochondrial DNA (NUMT) landscapes in stink bugs of the family Pentatomidae","authors":"He Wu,&nbsp;Yunbin Li,&nbsp;Rentao Liao,&nbsp;Jiaxin Zhang,&nbsp;Youshou Gao,&nbsp;Gang Chen,&nbsp;Wei Ren,&nbsp;Zichao Mao,&nbsp;Zhengjie Liu","doi":"10.1007/s10142-026-01875-3","DOIUrl":"10.1007/s10142-026-01875-3","url":null,"abstract":"<div><p>Pentatomidae stink bugs comprise ecologically diverse lineages, including predatory and phytophagous taxa, yet comparative data on their mitochondrial genome architecture and nuclear mitochondrial DNA segments (NUMTs) remain limited. Here, we report a high-quality mitochondrial genome assembly for the predatory stink bug <i>Eocanthecona furcellata</i> (Asopinae) and conduct comparative analyses with the predatory <i>Arma custos</i> (Asopinae) and the phytophagous <i>Nezara viridula</i> (Pentatominae). The mitochondrial genome of <i>E. furcellata</i> exhibits the typical insect gene complement and conserved organization, including canonical protein-coding genes, rRNAs and tRNAs, with nucleotide composition and codon usage patterns consistent with other pentatomids. We identified a conservative set of high-confidence NUMTs in the <i>E. furcellata</i> nuclear genome and characterized their genomic distribution and flanking gene contexts. Transcriptomic comparisons between early instar nymphs and adults of <i>E. furcellata</i> revealed stage-associated differences in the expression of mitochondrial function-related genes. Comparative analyses across <i>E. furcellata</i>, <i>A. custos</i>, and <i>N. viridula</i> suggested broadly conserved mitochondrial genome organization, alongside lineage-associated variation in nucleotide composition, NUMT distribution, and curated orthologous genes involved in core mitochondrial energy metabolism. Together, this study provides foundational genomic resources and a comparative framework for understanding mitochondrial genome evolution and NUMT dynamics in Pentatomidae. Future studies incorporating congeneric species and phylogenetically matched sampling designs will be necessary to disentangle lineage effects from ecological divergence.</p></div>","PeriodicalId":574,"journal":{"name":"Functional & Integrative Genomics","volume":"26 1","pages":""},"PeriodicalIF":3.1,"publicationDate":"2026-05-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147829508","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 insights into Rhizobium anhuiense IY2 isolated from Trifolium caudatum root nodules","authors":"Volkan Eroğlu,&nbsp;Asiye Esra Eren Eroğlu,&nbsp;İhsan Yaşa","doi":"10.1007/s10142-026-01874-4","DOIUrl":"10.1007/s10142-026-01874-4","url":null,"abstract":"<div><p>Nitrogen fixing Rhizobia play an important role in legume growth and sustainable agriculture, and genome based analyses have become essential for understanding the genetic basis of their symbiotic traits and functional potential. Here, <i>Rhizobium</i> anhuiense strain IY2 was isolated from the root nodules of the endemic legume Trifolium caudatum and characterized using 16 S rRNA and whole-genome sequencing. The genome, sequenced via the Illumina NovaSeq 6000 platform, spans 6,917,460 bp with approximately 6,900 predicted coding sequences (CDSs). Genomic analysis suggested the presence of various genetic determinants potentially linked to plant growth promotion, including those involved in iron acquisition, nitrogen metabolism, stress response, and auxin biosynthesis. While no CRISPR arrays were detected, two prophage regions were identified. Bioinformatic screening via the CARD database identified 47 AMR-related sequences, primarily comprising putative efflux systems and antibiotic targets rather than confirmed resistance determinants. The genome also harbors <i>nod</i>, <i>nif</i>, and <i>fix</i> gene clusters, indicating the genomic potential for symbiotic nitrogen fixation (SNF). Phylogenetic analysis of the nodC amino acid sequence supports a host-specific symbiotic relationship with <i>Trifolium</i> species. Notably, the presence of two distinct copies of the <i>nodD</i> gene suggests a potential for broad host range and strong symbiotic adaptability. This study provides the first genomic insights into the symbiotic association between a rhizobial species and <i>T. caudatum</i>, a legume endemic to Turkey.</p></div>","PeriodicalId":574,"journal":{"name":"Functional & Integrative Genomics","volume":"26 1","pages":""},"PeriodicalIF":3.1,"publicationDate":"2026-05-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s10142-026-01874-4.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147829506","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":"The sleeping kidney: microRNA expression profiling of kidney tissue during daily torpor in mice","authors":"Panyi Yang,&nbsp;Saif Rehman,&nbsp;Jing Zhang,&nbsp;Ziyin Wang,&nbsp;Zihan Zhao,&nbsp;Bofang Zhang,&nbsp;Kenneth B. Storey,&nbsp;Yuhong Hu,&nbsp;Hui Wang","doi":"10.1007/s10142-026-01873-5","DOIUrl":"10.1007/s10142-026-01873-5","url":null,"abstract":"<div><p>MicroRNA (miRNA), a class of short non-coding RNA, serves as a metabolically cheap and fast acting mechanism to inhibit translation of complementary mRNA. These molecules play a central role in regulating metabolic changes during torpor in small mammals, such as the house mouse (<i>Mus musculus</i>). The present study sequenced mouse kidney RNA to identify changes in miRNA expression in kidney, comparing active control mice (C57BL/6 strain) with mice in varying stages of torpor. Out of a total 962 miRNAs, 82 were differentially expressed when comparing torpid states to the control with 65, 14, and 2 miRNAs differentially expressed in deep torpor, early torpor, and recovery from torpor mice, respectively. In silico analysis of these targets demonstrated a clear downregulation of gene sets associated with cancer and active metabolism. This suggests that miRNA may play important roles in suppressing cell division and proliferation during torpor, along with maintaining a hypometabolic state. Machine learning techniques identified two specific miRNAs (miR-101c, miR-101a-3p) that can strongly distinguish between torpid and active states in kidney among other differentially regulated miRNA. The present study highlights the role of miRNA in transcriptional regulation of cell signaling and metabolic pathways in kidney throughout mouse torpor.</p></div>","PeriodicalId":574,"journal":{"name":"Functional & Integrative Genomics","volume":"26 1","pages":""},"PeriodicalIF":3.1,"publicationDate":"2026-05-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147829507","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":"Integrative characterization of tissue-specific 3D genome organization and associated transcriptional regulation in pig liver and muscle","authors":"Weiwei Zhou,&nbsp;Yani Huang,&nbsp;Chenyu Li,&nbsp;Mei Ge,&nbsp;Mingfang Zhou,&nbsp;Huashui Ai,&nbsp;Zhiyan Zhang","doi":"10.1007/s10142-026-01872-6","DOIUrl":"10.1007/s10142-026-01872-6","url":null,"abstract":"<div><p>Higher-order chromatin organization plays an important role in gene regulation; however, its tissue-specific features and regulatory relationships remain to be systematically characterized. In this study, we constructed high-resolution three-dimensional (3D) genome maps of pig liver and muscle by integrating Hi-C data with ATAC-seq, ChIP-seq, and RNA-seq datasets. Tissue-differential 3D structures, including compartments, topologically associating domains (TADs), and chromatin loops, exhibited limited spatial overlap and did not show a strictly coordinated hierarchical cascade among these structural layers. We systematically characterized the epigenetic modification features associated with different hierarchical levels of 3D chromatin structure and further analyzed their associations with gene expression. At a subset of genomic loci, compartment status, TAD organization, and enhancer-promoter interactions exhibited coordinated spatial patterns, suggesting that multi-layered chromatin organization might be associated with gene regulation. Further analyses showed that tissue-specific loop anchors tended to be enriched for tissue-specific transcription factors (TFs), and their presence was associated with stronger chromatin interaction signals and higher gene expression levels compared with anchors lacking such binding sites. Our results also supported the possibility that the formation of some tissue-specific chromatin loops was associated with chromatin accessibility, active histone modifications, and coordinated TF enrichment, rather than being entirely dependent on CTCF enrichment. Overall, these results provided a useful reference for understanding tissue-specific gene regulation in mammals and provided a foundational data resource for future functional genomics studies in livestock.</p></div>","PeriodicalId":574,"journal":{"name":"Functional & Integrative Genomics","volume":"26 1","pages":""},"PeriodicalIF":3.1,"publicationDate":"2026-05-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147796825","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":"Association of MUC3A P258S mutation with advanced phase CML structural and in silico insights","authors":"Sameen Shahid,&nbsp;Zafar Iqbal,&nbsp;Muhammad Abbas Khokhar,&nbsp;Muhammad Farooq Sabar","doi":"10.1007/s10142-026-01871-7","DOIUrl":"10.1007/s10142-026-01871-7","url":null,"abstract":"<div><p>Chronic Myeloid Leukemia (CML) is primarily driven by the BCR-ABL fusion oncogene, yet the mechanisms underlying progression to advanced phases remain unclear. Through Sanger sequencing of 22 CML patients, we identified a novel missense mutation in MUC3A (3025 C &gt; T; P258S) exclusively in advanced-phase cases. PCR amplification and Sanger sequencing confirmed its presence, while control and chronic-phase patients lacked the variant. Structural and physicochemical analyses revealed that the P258S substitution alters protein stability, secondary structure, and conformational flexibility. Molecular docking of 22 DrugBank ligands demonstrated enhanced binding affinity of the mutant protein, particularly with Capmatinib, which was further validated by molecular dynamics simulations showing increased flexibility and compactness. Principal component analysis and hydrogen bond profiling supported significant dynamic changes in the mutant structure. Collectively, these findings suggest that MUC3A P258S acts as a potential candidate biomarker of CML progression and influences therapeutic response, highlighting Capmatinib and related inhibitors as candidates for drug repurposing in hematological malignancies. To our knowledge, this is the first report implicating MUC3A in leukemia biology, extending its role beyond epithelial cancers. </p></div>","PeriodicalId":574,"journal":{"name":"Functional & Integrative Genomics","volume":"26 1","pages":""},"PeriodicalIF":3.1,"publicationDate":"2026-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147796340","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":"Oncogenic DCTPP1/MYC feedback loop rewires pyrimidine metabolism to drive hepatocellular carcinoma","authors":"Jing Li,&nbsp;Juan Liang,&nbsp;Meigui Zhang,&nbsp;Ruixia Ma,&nbsp;Ruili Zhou,&nbsp;Jiahui Xi,&nbsp;Haiying Yu,&nbsp;Yonghong Li,&nbsp;Chenyu Wang,&nbsp;Zhongtian Bai","doi":"10.1007/s10142-026-01870-8","DOIUrl":"10.1007/s10142-026-01870-8","url":null,"abstract":"<div><p>Nucleotide metabolic dysregulation fuels tumor proliferation, yet its drivers in hepatocellular carcinoma (HCC) remain poorly defined. DCTPP1, a dCTP pyrophosphohydrolase linked to aggressive cancers, is overexpressed in HCC but its regulatory role is unknown. Here, integrated analyses of clinical databases and tissue microarrays revealed that high DCTPP1 expression correlates with poor prognosis in HCC patients. Functional studies demonstrated that DCTPP1 knockdown suppresses HCC proliferation, migration, and tumorigenesis in vitro and in vivo. Mechanistically, we uncovered a novel DCTPP1-MYC positive feedback loop: MYC transcriptionally activates DCTPP1, while DCTPP1 modulates MYC protein levels, potentially through the Wnt/β-catenin signaling pathway. This circuit selectively disrupts pyrimidine metabolic enzymes (CTPS1, TYMS, TK1, NME1), destabilizing the dNTP pool and accelerating HCC progression. Our work identifies DCTPP1 as an oncogenic metabolic driver in HCC, revealing a targetable vulnerability for nucleotide metabolism-directed therapy.</p></div>","PeriodicalId":574,"journal":{"name":"Functional & Integrative Genomics","volume":"26 1","pages":""},"PeriodicalIF":3.1,"publicationDate":"2026-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147796338","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":"PlantGATA: a comprehensive database for plant GATA transcription factors","authors":"Mangi Kim","doi":"10.1007/s10142-026-01855-7","DOIUrl":"10.1007/s10142-026-01855-7","url":null,"abstract":"<div><p>Plant GATA transcription factors (TFs) are a conserved family of regulatory proteins characterized by a GATA zinc finger (CX₂CX_18-20CX₂C) that binds WGATAR (W = A/T, R = A/G) motifs. The growing availability of plant genome resources has facilitated large-scale comparative analyses of GATA TFs, underscoring the need for systematic cross-species characterization. However, most existing studies remain manual and methodologically heterogeneous, limiting the scalability, consistency, and interpretability of comparative analyses. To address these challenges, this study presents PlantGATA (https://plantgata.vercel.app/), a comprehensive database built on a standardized pipeline that curates 13,969 GATA TFs (11,109 loci) from 374 plant genomes spanning 174 species, 124 genera, 63 families, 40 orders, and 12 taxonomic groups. The database offers interactive genome-wide browsers for cross-species comparison of GATA TF repertoires, integrating multi-level structural and functional features within a hierarchical taxonomic framework. In addition, PlantGATA integrates curated reference resources, including 16 experimentally validated GATA TFs, 700 high-confidence functionally annotated GATA TFs, and 65 genome-wide GATA TF identification studies, establishing a robust framework for functional classification and comparative genomics. Collectively, PlantGATA provides an integrated platform for structural and functional analysis of plant GATA TFs, supporting efficient large-scale comparative research.</p></div>","PeriodicalId":574,"journal":{"name":"Functional & Integrative Genomics","volume":"26 1","pages":""},"PeriodicalIF":3.1,"publicationDate":"2026-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147796339","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}