Search Results (1,886)

The TP63 locus generates TAp63 and ΔNp63 isoforms through alternative promoter usage, but the cis-regulatory features that confer differential promoter responsiveness remain incompletely defined. Here, we functionally dissected distal TAp63-associated and proximal ΔNp63-associated TP63 promoter regions using reporter-based assays in A549 cells. Rabbit TP63 promoter fragments were selected from distal and proximal promoter-associated regions and analyzed by serial deletion and site-directed mutagenesis. Deletion mapping identified discrete promoter intervals that positively or negatively affected reporter activity, while motif perturbation revealed promoter-context-dependent contributions of predicted FOXA1/2, NKX2–1, SOX9, and TP63-related regulatory elements. Endogenous ChIP-qPCR at corresponding human TP63 promoter-associated regions provided local enrichment evidence for selected transcription-factor-associated signals, and FOXA2 or SOX9 depletion shifted endogenous TAp63 and ΔNp63 protein abundance. These findings identify candidate TP63 promoter intervals and transcription-factor-responsive motifs that differentially affect dual-promoter reporter output. The study provides a promoter-level framework for investigating how TP63 promoter responsiveness is influenced by promoter architecture, motif composition, and cellular regulatory background within a heterologous reporter context, while highlighting the need for future validation in more physiological human epithelial systems. Full article

Background and Objective: The objective of this exploratory study was to identify the molecular characteristics that influence survival outcomes in cases of cervical adenocarcinoma, utilising data from the TCGA (The Cancer Genome Atlas) database. Methods: The ‘TCGA Firehose Legacy’ dataset was accessed through the Cbioportal website. SILVA invasion patterns were independently evaluated on digitized whole-slide images by two gynecologic pathologists. Cases were categorized by overall survival status (living vs. deceased). Somatic mutations, copy number alterations, mRNA expression, RPPA protein expression, and DNA methylation profiles were analyzed. Survival analyses were performed using Kaplan–Meier methods and log-rank tests, supplemented by differential analysis. Pathway and transcription factor binding motif enrichment was evaluated via g:Profiler. p and q < 0.05 were considered statistically significant. Results: Among 27 cases (22 living, 5 deceased; 23 HPV-positive, 2 HPV-negative, 2 unknown), PREX1 protein expression was identified as the top-ranked differentially expressed candidate protein (p = 4.29 × 10⁻⁵, q = 8.70 × 10⁻³). Kaplan–Meier analysis demonstrated superior overall survival in patients with high PREX1 protein levels. DNA methylation analysis identified 8 differentially methylated genes (p, q < 0.05); 7 were hypermethylated in the deceased group (MCEMP1, RNASE2, RINL, CCL17, THBD, SFXN5, PRR19), while WDR89 was hypermethylated in the living group. Enrichment analysis of differentially methylated promoter regions revealed a distinct KLF9-binding regulatory motif (q = 0.032). Due to sample size constraints (n = 2 HPV-negative, n = 2 SILVA Pattern A), subgroup comparisons for HPV status and SILVA patterns were interpreted descriptively without inferential statistical claims. Conclusions: In this exploratory cohort, elevated PREX1 protein levels and promoter hypermethylation of specific immune- and metabolic-related genes were associated with overall survival in endocervical adenocarcinoma. Due to the current lack of independent public proteomic validation datasets, PREX1 emerges as a novel candidate biomarker requiring prospective tissue-based immunohistochemical and epigenetic validation in larger multi-center clinical cohorts. Full article

Background: Domain of Unknown Function 1645 (DUF1645) is a conserved but poorly characterized plant gene family whose evolutionary history and roles in stress adaptation remain unclear. We performed an integrated genomic, evolutionary, transcriptomic, and Quantitative Trait Locus (QTL) characterization of the DUF1645 family in rice (Oryza sativa). Methods and Results: We identified 14 intronless, non-redundant OsDUF1645 genes distributed across eight chromosomes. Phylogenetic and collinearity analyses suggested that family expansion within Poaceae involved ancestral segmental and localized tandem duplication events. Promoter analysis identified stress- and phytohormone-responsive cis-acting elements, including ABRE, MBS, and MeJA-associated motifs. Public transcriptome datasets revealed diverse OsDUF1645 expression patterns under abiotic and hormonal treatments. Integration with the Quantitative Trait Loci Annotation Rice Online (Q-TARO) QTLome identified physical co-localization of multiple OsDUF1645 loci with stress- and agronomic-trait QTLs, including salinity-, drought-, root architecture-, and water-deficit-associated regions. On Chromosome 1, OsDUF1645.1, OsDUF1645.2, OsDUF1645.3, and OsDUF1645.4 overlapped QTL intervals associated with salinity-related physiological traits, including Na⁺ uptake and Na⁺ balance, and drought-related root traits. On Chromosome 5, the tandemly arranged OsDUF1645.8, OsDUF1645.9, and OsDUF1645.10 co-localized with QTLs related to root architecture and water-deficit responses. qRT-PCR validation under salinity, osmotic stress, and cadmium exposure confirmed distinct stress-responsive expression profiles; OsDUF1645.6 exhibited broad multi-stress responsiveness, whereas OsDUF1645.3 was downregulated under several conditions. Conclusions: The OsDUF1645 family exhibits substantial functional diversification, supported by distinct regulatory architectures, expression profiles, and QTL associations. These findings provide a framework for prioritizing OsDUF1645 candidates for functional validation and their potential application in molecular breeding and development of climate-resilient rice cultivars. Full article

The plant hormone abscisic acid (ABA) plays a crucial role throughout the plant life cycle and in adaptive responses to environmental stresses. The pyrabactin resistance 1-like (PYR/PYL/RCAR) proteins act as key regulators in the ABA signal transduction pathway by functioning as direct receptors for ABA. Although PYL genes have been identified in a variety of plant species, their evolutionary and structural characteristics in tomatoes (Solanum lycopersicum) remain elusive. To address this gap, we identified nine SlPYL genes, which were classified into three subfamilies: I (two genes), II (three genes), and III (four genes), and their encoded proteins were predicted to be primarily localized in the cytosol and chloroplast. Structural analysis revealed diverse exon–intron organizations along with five conserved motifs. All identified SlPYLs contained the START domain (PF10604), validating their identity as actual PYL proteins. Prediction of cis-acting regulatory elements in SlPYL’s promoter regions was found to be associated with light responsiveness, hormone signaling, stress responses, and plant growth and development. Prediction of post-translational modification sites indicated that SlPYLs are predominantly phosphorylated and acetylated at serine and lysine residues, respectively. Tertiary structure modeling demonstrated conserved three-dimensional architectures among SlPYL proteins, supporting their functional conservation. Expression profiling revealed that specific SlPYL genes exhibit distinct expression patterns across different tissues (root, leaf, and bud) following ABA treatment, indicating functional diversification. Considering the well-established negative correlation between ABA accumulation and bud outgrowth, the ABA-induced differential expression (3~5-fold) of some SlPYL genes (SlPYL3, SlPYL4, SlPYL7, and SlPYL8), particularly in bud tissues after 24 hpt, suggests a potential role in ABA-mediated suppression of bud outgrowth. However, these functional inferences are primarily based on genome-wide computational analyses and expression profiling and therefore require further experimental validation. Full article

Nucleotide motifs in the core promoters of eukaryotic protein-coding genes transcribed by RNA polymerase II (Pol II) play an important role in the transcription process. We analyzed the role of an octanucleotide located in the TATA box position. Depending on whether this octanucleotide can form a complex with the TATA-binding protein (TBP), the promoter is classified as either TATA-containing or TATA-less. We analyzed the differences in the primary and spatial structures, as well as their dynamics, in TATA-containing and TATA-less promoters of mammals and plants. We divided the complete promoter sets of six organisms (H. sapiens, M. musculus, C. familiaris, A. thaliana, Z. mays, and H. vulgare) from the EPDnew database into TATA-containing and TATA-less fractions. The sizes of the TATA-containing promoter fractions are significantly smaller than those of the TATA-less fractions in all studied organisms, except in A. thaliana, where the sizes of both fractions are approximately equal. We characterized promoter architecture using variation profiles of various base-pair step parameters, minor-groove width, and the conformational dynamics of native DNA. The architectures of TATA-containing and TATA-less promoters differ significantly. The possible mechanistic influence of DNA structural features on the formation of the pre-initiation complex (PIC) in both types of promoters is discussed. Full article

SLAMF1 encodes CD150, an immunoregulatory receptor involved in lymphocyte activation, T–B-cell interactions, and humoral immune responses. The SLAMF1 promoter polymorphism rs2295613(G>A) was previously associated with systemic lupus erythematosus (SLE) susceptibility in a Chinese case–control cohort. Here, we investigated the regulatory activity of rs2295613 in the transformed B-cell lines Raji and MP1 and in primary human CD19⁺ B cells. The rs2295613(A)-containing reporter showed higher promoter activity than the rs2295613(G)-containing reporter in all three cellular systems. Bioinformatic analysis predicted that the G to A substitution strengthens a pre-existing MYC-compatible motif. Substitutions disrupting the motif-containing region attenuated the rs2295613(A)-associated increase in reporter activity and reduced enrichment of the promoter fragment in anti-c-MYC DNA pull-down assays. Partial siRNA-mediated reduction in MYC mRNA also decreased the activity of the rs2295613(A)-containing reporter in Raji cells. Together, these findings identify rs2295613 as a functional SLAMF1 promoter variant in B-cell reporter systems and support a contribution of c-MYC-associated regulation to the enhanced activity of the rs2295613(A)-containing promoter. Full article

Sulfated polysaccharides from red seaweeds are emerging as versatile bioactive macromolecules. Here, we report that funoran-type galactans from Gelidiopsis variabilis (GV) function as immunometabolic reprogrammers, orchestrating inflammation resolution through targeted remodeling of amino acid and fatty acid metabolism in macrophages, potentially via receptor-mediated pathways. Cold and hot water extraction yielded structurally distinct fractions (360–3006 kDa) characterized by NMR as sulfated galactans with κ-carrageenan motifs and variable sulfation (6.6–21.5%). In RAW264.7 macrophages, fractions GV-1A and GV-2A induced an anti-inflammatory metabolic state characterized by arginine accumulation (from 4.61% to 7.06% of the total amino acid pool), reduced ornithine levels, and complete the elimination of pro-inflammatory myristate (14:0), while upregulating phagocytosis (149% of control). In a carrageenan-induced paw edema model, GV-1A and GV-2A dose-dependently upregulated pro-resolution markers (IL-10, IL-4, TGF-β1, Arg1, HO-1), outperforming the standard drug meloxicam. While the in vitro arginine accumulation suggests functional arginase inhibition, the in vivo Arg1 upregulation reflects a transcriptional response in a complex tissue environment. We propose that these findings collectively support a ‘resolution-phase metabolic phenotype’, a working model whereby GV polysaccharides reprogram macrophage metabolism toward inflammation resolution through context-dependent mechanisms. These findings establish G. variabilis polysaccharides as metabolically active immunomodulators that promote inflammation resolution, with the potential for applications in inflammatory diseases and as a pharmaceutical platform for drug development. Full article

G. barbadense represents an indispensable germplasm resource for high-quality textile fiber and disease resistance; nevertheless, systematic information regarding its ZRT/IRT-like protein (ZIP) gene family remains limited. Here, a total of 46 GbZIP genes were identified across the G. barbadense genome. Comprehensive bioinformatic investigations revealed uneven chromosomal distribution and confirmed that segmental/whole-genome duplications, supplemented by localized tandem duplications, drove family expansion. Members clustered within the same phylogenetic clades shared conserved motif organization and gene architecture, while promoter regions harbored abundant cis-acting elements associated with phytohormone and stress signaling. Transcriptome profiling indicated distinct expression patterns across vegetative/reproductive tissues, fiber and ovule developmental stages, and diverse abiotic stress conditions (cold, hot, drought, and salt). Quantitative Real-Time PCR (qRT-PCR) further validated that several GbZIP candidates exhibited temporal expression variations upon exposure to cadmium toxicity, V. dahliae infection, and combined Cd-V. dahliae stress. Specifically, GbZIP13, GbZIP18, GbZIP27, and GbZIP36 displayed prominent broad-spectrum responses to all three stress conditions, whereas GbZIP16, GbZIP29, and GbZIP30 showed stress-specific regulatory divergence. Overall, this study aims to systematically analyze the evolutionary characteristics and expression patterns of the GbZIP family, and to specifically evaluate the response differences under Cd stress, V. dahliae stress, and combined stress, in order to identify potential key candidate genes. Full article

Cell-wall polysaccharide O-acetylation contributes to cell-wall assembly, organ development, and plant–pathogen interactions, but the cucumber TBL gene family remains poorly characterized. Here, 37 CsTBL genes were identified genome-wide and analyzed using phylogenetic, syntenic, conserved-motif, gene-structure, promoter, protein-structure, Gene Ontology, and transcriptome approaches, followed by RT-qPCR analysis after powdery mildew inoculation. All CsTBL proteins contained the conserved GDS and DxxH motifs, whereas accessory motifs and predicted structural features varied among clades. Intraspecific analysis identified dispersed, WGD/segmental, and tandem duplication categories, and cross-species synteny was more extensive with melon than with Arabidopsis. Homology-derived annotations associated CsTBL genes with cell-wall polysaccharide metabolism, Golgi/endomembrane compartments, and O-acetyltransferase activity, including six genes assigned to xylan O-acetyltransferase-related annotations. Expression profiling revealed tissue- and developmental-stage-dependent patterns, whereas the publicly available powdery mildew RNA-seq dataset provided descriptive temporal expression profiles in Podosphaera xanthii-inoculated samples. Independent RT-qPCR analysis using time-matched mock controls revealed distinct post-inoculation responses among six selected genes. Relative to the corresponding mock controls, CsTBL2 was consistently repressed; CsTBL15 showed transient induction at 1 dpi followed by repression; CsTBL24 exhibited a biphasic response; CsTBL25 was induced at all sampled post-inoculation time points; CsTBL26 showed progressive induction; and CsTBL30 reached its highest observed expression level at 3 dpi. Integrated functional annotation and expression evidence highlighted CsTBL26 as a priority candidate for further functional characterization, while CsTBL24 and CsTBL25 represented fruit-associated candidates with distinct powdery mildew responses; CsTBL30 remained an additional strongly infection-responsive candidate. These findings provide an evolutionary and expression-based framework for the functional characterization of the cucumber TBL gene family. Full article

Wheat (Triticum aestivum), a key global crop, faces rising drought stress that limits root growth and water uptake. Root meristem growth factors (RGFs) are small peptides that regulate root stem cell maintenance, meristem activity, and lateral root formation in model plants, yet the RGF gene family remains unexplored in wheat. Here, we performed a comprehensive genome-wide analysis of the TaRGF gene family, identifying 15 genes distributed across the A, B, and D subgenomes and classified into five homeologous groups (TaRGF1–TaRGF5), predominantly located on chromosomes 2 and 6. All TaRGFs contained a characteristic RGF motif, with dibasic cleavage sites and Asp–Tyr motifs indicating conserved maturation mechanisms. Based on the phylogenetic analysis, the TaRGF5 homeologs showed the highest similarity to Arabidopsis thaliana RGF5. Tested RNA-seq data revealed predominantly root-enriched expression for all TaRGF genes, with TaRGF5 exhibiting the most root-preferential and downregulation under drought stress. Quantitative real-time PCR (qRT-PCR) confirmed that drought stress suppressed the expression of TaRGF5A, TaRGF5B, and TaRGF5D in roots of wheat cultivar Sids-13 across all time points, unlike the higher accumulation seen in controls. Promoter analysis predicted a unique BES1 transcription factor binding site exclusively in TaRGF5B, linking brassinosteroid signaling to peptide-mediated root regulation. Structural modeling and molecular docking predicted an interaction between wheat TaRGF5 homeologs and root growth factor-insensitive receptor kinase (TaRGI3), characterized by conserved sulfotyrosine-mediated binding and favorable interaction energetics. Based on this characterization of the wheat RGF gene family, particularly the potential role of TaRGF5 in root development and drought-adaptation signaling, we propose targeting this gene for functional analysis to improve wheat resilience under water-limited conditions. Full article

Background/Objectives: Dehydrins (DHNs) are late embryogenesis abundant proteins that play protective roles under water-deficit conditions; however, their organization and function remain unexplored in sesame (Sesamum indicum), an important oilseed crop frequently cultivated in arid and semi-arid regions. This study aimed to identify and characterize the DHN gene family in sesame and evaluate the expression of its members under drought stress. Methods: Genome-wide identification was performed using the Dehydrin domain HMM profile, followed by phylogenetic analysis, conserved motif and gene structure characterization, synteny analysis, promoter cis-element profiling, and secondary/tertiary structure prediction. Transcriptional responses were profiled by qPCR in two sesame cultivars (drought-sensitive and drought-tolerant) under PEG-induced osmotic stress at germination and seedling stages. Results: Four DHN genes were identified, spanning three phylogenetic subfamilies (I–III) and three DHN subclasses: SK_n (SiDHN1/2), Y_nK_n (SiDHN3), and Y_nSK_n (SiDHN4). SiDHN1 and SiDHN2 likely arose from a segmental duplication, and a single conserved syntenic pair was found between SiDHN4 and olive (Olea europaea). Secondary structure predictions uncovered contrasting structural propensities: SiDHN1/2 are predicted to be α-helix-rich, partially ordered proteins (41–44% predicted α-helix), whereas SiDHN3/4 are predicted to be predominantly intrinsically disordered (~75–80% random coil). SiDHN3 was consistently upregulated across all conditions (1.84–9.12-fold), while SiDHN4 exhibited strong genotype-specific induction of 9.39-fold exclusively in the drought-tolerant cultivar during germination. Conclusions: The sesame DHN family achieves functional breadth through structural diversification—an ordered–disordered continuum mirrored by divergent expression programming—rather than through numerical expansion. SiDHN3 and SiDHN4 are identified as primary candidates for drought tolerance improvement in sesame. Full article

Background: Autophagy plays a central role in maintaining cellular homeostasis, regulating growth and development, and responding to multiple stresses. Autophagy-related genes (ATGs) play critical roles in autophagy, yet their functional diversity in soybean (Glycine max) remains underexplored. Methods: Genome-wide identification of GmATG genes was performed using sequence similarity and domain-based searches against the Wm82.gnm4 reference genome, followed by characterization of physicochemical properties, chromosomal distribution, phylogenetic relationships, gene duplication, conserved motifs, gene structure, three-dimensional structural, and promoter cis-acting elements. Tissue-specific expression and multiple stresses response were examined using transcriptome data and profiled by RT-qPCR. Results: A total of 60 GmATG genes belonging to 20 subfamilies were identified in soybean. Gene family expansion was predominantly driven by fragment duplication (33 gene pairs), with the ATG8 family expanding to 12 members, and pan-genomic analysis uncovered prominent copy number variation (6–9 copies) in the ATG18 family. GmATG genes showed distinct expression patterns in response to multiple abiotic and biotic stresses. Specifically, GmATG18f was significantly induced by phosphorus deficiency in the low-phosphorus-tolerant soybean variety Nannong 94-156. GmATG8g, GmATG9d and GmATG13d showed a typical expression trend of initial increase followed by decrease, with expression levels peaking at 6–12 h after salt stress treatment. GmATG8g and GmATG9d were rapidly upregulated at the early drought stress stage, while GmATG13a maintained sustained upregulation. In response to Phomopsis stem rot, GmATG7a/8h/8i/11/13d/18e/18f displayed differential expression in resistant and susceptible soybean materials. Conclusions: This study systematically characterizes the composition, expansion and stress response patterns of the GmATG gene family, revealing functional differentiation among family members. The identified key candidate genes, including abiotic-stress-regulated GmATG8g/9d/13d/18f and biotic-stress-regulated GmATG7a/8h/8i/11/13d/18e/18f, provide valuable genetic resources for the molecular breeding of stress-tolerant soybean. Full article

Betaine aldehyde dehydrogenase (BADH) catalyzes the final step in glycine betaine biosynthesis, but the evolutionary divergence and differential salt responsiveness of BADH homeologs in bread wheat remain unclear. We identified six TaBADH genes and analyzed their phylogenetic relationships, conserved motifs, gene structures, promoter cis-acting elements and synteny. RNA-seq and qRT-PCR were used to compare expression in salt-tolerant Jimai 60 and salt-sensitive Chinese Spring under 200 mM NaCl, and BADH activity, glycine betaine, H₂O₂ and malondialdehyde (MDA) were measured during treatment. The genes separated into chromosome group 2 and group 6 clades with distinct structural and transcriptional patterns. TaBADH-2B encoded a shorter protein and lacked several conserved motifs. Group 6 genes showed stronger salt-responsive expression in Jimai 60, with TaBADH-6D displaying the strongest and most sustained induction. Jimai 60 also showed higher BADH activity and glycine betaine accumulation and lower H₂O₂ and MDA contents at later time points. Expression of TaBADH-6D improved E. coli growth under 200 mM NaCl. These findings identify homeolog-specific divergence within the BADH wheat family and support TaBADH-6D as a candidate for plant-level functional validation. Full article

Pinoresinol–lariciresinol reductase (PLR) catalyzes a key reductive step in plant lignan biosynthesis. Although flax (Linum usitatissimum L.) seeds are rich in lignans, the PLR gene family and its relationship with lignan accumulation during seed development remain insufficiently characterized. Here, 18 LuPLR genes were identified from the telomere-to-telomere genome assembly of the flax cultivar ‘Gaosi’ using BLASTP and HMMER searches. Their phylogenetic relationships, gene structures, conserved motifs, chromosomal distribution, duplication and syntenic relationships, promoter cis-acting elements, predicted microRNA targets, and expression profiles were analyzed. Seed lignan content at 5, 10, 20, 30, and 40 days after flowering was quantified by high-performance liquid chromatography, and candidate genes were screened using quantitative real-time PCR and Pearson correlation analysis. The LuPLR genes were unevenly distributed across eight chromosomes and exhibited substantial structural and regulatory diversity. Seed lignan content varied dynamically and reached its highest level at 40 days after flowering. LuPLR10, LuPLR11, and LuPLR16 showed positive correlations with lignan content. Among them, LuPLR10 was prioritized because its developmental expression pattern most closely paralleled lignan accumulation. Subcellular localization analysis indicated that the LuPLR10 protein was predominantly associated with chloroplasts. These findings provide a genomic framework for the flax PLR family and identify LuPLR10 as a priority candidate for further functional investigation. Full article

Carboxylesterases (CXEs) participate in diverse plant metabolic processes, including isoflavone biosynthesis. However, the soybean GmCXE subfamily remains poorly characterized, especially in relation to root isoflavone accumulation and the response to Fusarium oxysporum. Here, fifty-six putative GmCXE genes were identified in the soybean genome and classified into three major phylogenetic clades. Analyses of gene structure, conserved motifs, protein domains, and promoter cis-elements revealed conserved features as well as potential functional divergence among subfamily members. Collinearity and duplication analyses indicated that segmental duplication was the main driver of GmCXE subfamily expansion. Tissue-specific expression profiling and RT-qPCR validation selected five root-expressed genes as candidates associated with isoflavone accumulation. SNP variation analysis and allelic group analysis of 209 soybean accessions further prioritized GmCXE54 as a candidate gene for root isoflavone accumulation. Allelic groups defined by a putative promoter SNP, Chr.20-rs39215413, showed significant differences in root daidzein and total isoflavone contents, with accessions carrying the C allele exhibiting higher levels of both traits than those carrying the T allele. Functional analysis in soybean hairy roots showed that GmCXE54 overexpression increased daidzein and total isoflavone accumulation. At 3 h after F. oxysporum inoculation, GmCXE2, GmCXE39, and GmCXE54 were induced, with GmCXE54 showing the strongest response in the resistant accession ZD27. These findings clarify GmCXE subfamily evolution and identify GmCXE54 as a candidate gene associated with root isoflavone accumulation and early F. oxysporum response, offering new perspectives for improving soybean isoflavone-related traits and investigating root response mechanisms. Full article