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Keywords = chromatin immunoprecipitation (ChIP)

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27 pages, 2494 KiB  
Review
Redox-Epigenetic Crosstalk in Plant Stress Responses: The Roles of Reactive Oxygen and Nitrogen Species in Modulating Chromatin Dynamics
by Cengiz Kaya and Ioannis-Dimosthenis S. Adamakis
Int. J. Mol. Sci. 2025, 26(15), 7167; https://doi.org/10.3390/ijms26157167 - 24 Jul 2025
Viewed by 433
Abstract
Plants are constantly exposed to environmental stressors such as drought, salinity, and extreme temperatures, which threaten their growth and productivity. To counter these challenges, they employ complex molecular defense systems, including epigenetic modifications that regulate gene expression without altering the underlying DNA sequence. [...] Read more.
Plants are constantly exposed to environmental stressors such as drought, salinity, and extreme temperatures, which threaten their growth and productivity. To counter these challenges, they employ complex molecular defense systems, including epigenetic modifications that regulate gene expression without altering the underlying DNA sequence. This review comprehensively examines the emerging roles of reactive oxygen species (ROS) and reactive nitrogen species (RNS) as central signaling molecules orchestrating epigenetic changes in response to abiotic stress. In addition, biotic factors such as pathogen infection and microbial interactions are considered for their ability to trigger ROS/RNS generation and epigenetic remodeling. It explores how ROS and RNS influence DNA methylation, histone modifications, and small RNA pathways, thereby modulating chromatin structure and stress-responsive gene expression. Mechanistic insights into redox-mediated regulation of DNA methyltransferases, histone acetyltransferases, and microRNA expression are discussed in the context of plant stress resilience. The review also highlights cutting-edge epigenomic technologies such as whole-genome bisulfite sequencing (WGBS), chromatin immunoprecipitation sequencing (ChIP-seq), and small RNA sequencing, which are enabling precise mapping of stress-induced epigenetic landscapes. By integrating redox biology with epigenetics, this work provides a novel framework for engineering climate-resilient crops through the targeted manipulation of stress-responsive epigenomic signatures. Full article
(This article belongs to the Section Molecular Biology)
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20 pages, 3053 KiB  
Article
ERRα and HIF-1α Cooperate to Enhance Breast Cancer Aggressiveness and Chemoresistance Under Hypoxic Conditions
by Dimas Carolina Belisario, Anna Sapino, Ilaria Roato, Amalia Bosia, Sophie Doublier and Serena Marchiò
Cancers 2025, 17(14), 2382; https://doi.org/10.3390/cancers17142382 - 18 Jul 2025
Viewed by 396
Abstract
Background/Objectives: HIF-1α and ERRα are both implicated in breast cancer progression, yet their functional interplay remains poorly understood. This study investigates their molecular crosstalk in the context of hypoxia-induced drug resistance. Methods: MCF-7 (estrogen receptor, ER-positive) spheroids and CoCl2-treated [...] Read more.
Background/Objectives: HIF-1α and ERRα are both implicated in breast cancer progression, yet their functional interplay remains poorly understood. This study investigates their molecular crosstalk in the context of hypoxia-induced drug resistance. Methods: MCF-7 (estrogen receptor, ER-positive) spheroids and CoCl2-treated SK-BR-3 (ER-negative) cells were used to model tumor hypoxia. Protein expression, coimmunoprecipitation, chromatin immunoprecipitation (ChIP), pharmacological inhibition, and siRNA-mediated gene silencing were employed to assess physical and functional interactions. Immunohistochemistry (IHC) on a tissue microarray (TMA) of 168 invasive breast carcinomas was performed to evaluate clinical relevance. Results: ERRα levels remained unchanged under hypoxia, while its coactivator, Peroxisome Proliferator-Activated Receptor Gamma Coactivator-1 α (PGC-1α), was upregulated. ERRα physically interacted with HIF-1α and was required for HIF-1 transcriptional activity under hypoxic conditions. ChIP assays showed that ERRα-driven overexpression of Permeability glycoprotein 1 (P-gp) and Vascular Endothelial Growth Factor (VEGF) was mediated by HIF-1α binding to the MDR1 and VEGF promoters. Inhibition or silencing of ERRα reversed P-gp overexpression and restored intracellular doxorubicin. TMA analysis confirmed the clinical correlation between ERRα, HIF-1α, and P-gp expression, highlighting the role of ERRα in hypoxia-induced drug resistance. ERRα expression was independent of ER status, suggesting an estrogen-independent function. Conclusions: This study identifies a novel physical and functional interaction between ERRα and HIF-1α that promotes chemoresistance in hypoxic breast tumors. Targeting ERRα may represent a promising therapeutic strategy to overcome drug resistance in aggressive, ER-independent breast cancer subtypes. Full article
(This article belongs to the Section Cancer Drug Development)
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23 pages, 10678 KiB  
Article
Effects of Angiotensin II Receptor 1 Inhibition by LCZ696 on the Acquisition and Relapse of Methamphetamine-Associated Contextual Memory
by Xiaofang Li, Zhiting Zou, Xiangdong Yang, Jinnan Lü, Xiaoyu Zhang, Jiahui Zhou, Dan Zhu, Xinshuang Gong, Shujun Lin, Zhaoying Yu, Zizhen Si, Wenting Wei, Yakai Xie and Yu Liu
Pharmaceuticals 2025, 18(7), 1016; https://doi.org/10.3390/ph18071016 - 8 Jul 2025
Viewed by 402
Abstract
Background/Objectives: Contextual memory associated with methamphetamine (METH) use contributes to relapse and persistence of addiction. Angiotensin II type 1 receptor (AT1R) signaling has been implicated in drug reinforcement. LCZ696, a clinically used combination of sacubitril (a neprilysin inhibitor) and valsartan (an AT1R antagonist), [...] Read more.
Background/Objectives: Contextual memory associated with methamphetamine (METH) use contributes to relapse and persistence of addiction. Angiotensin II type 1 receptor (AT1R) signaling has been implicated in drug reinforcement. LCZ696, a clinically used combination of sacubitril (a neprilysin inhibitor) and valsartan (an AT1R antagonist), may interfere with METH-associated memory through the modulation of dopaminergic pathways. Methods: Male C57BL/6J mice were tested in a conditioned place preference (CPP) paradigm to assess the effects of LCZ696, sacubitril (AHU377), and valsartan on METH-induced memory expression and reinstatement. Synaptic plasticity in the nucleus accumbens (NAc) was examined by assessing the levels of synaptophysin (Syp) and postsynaptic density protein 95 (Psd95), as well as dendritic spine density. Dopaminergic signaling in the ventral tegmental area (VTA) was evaluated via ELISA, Western blotting, and chromatin immunoprecipitation (ChIP), targeting cAMP response element-binding protein (Creb) binding to the tyrosine hydroxylase (Th) promoter. To further assess the role of Th, an adeno-associated virus (AAV9) carrying a CRISPR-Cas9-based sgRNA targeting Th (AAV9-Th-sgRNA) was microinjected into the VTA. Results: LCZ696 and valsartan significantly reduced METH-induced CPP and reinstatement. LCZ696 reversed METH-induced synaptic and dopaminergic alterations and suppressed Creb-mediated Th transcription. Th knockdown attenuated both CPP acquisition and relapse. Conclusions: LCZ696 disrupts METH-associated contextual memory by modulating dopaminergic signaling and Creb-dependent Th expression, supporting its potential as a treatment for METH use disorder. Full article
(This article belongs to the Section Pharmacology)
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10 pages, 975 KiB  
Communication
Tryptophan Metabolite ITE Attenuates LPS-Induced MMP-9 via NF-κB/AP-1 in Monocytes
by Fatemah Bahman, Nadeem Akhter, Shihab Kochumon, Fahd Al-Mulla and Rasheed Ahmad
Int. J. Mol. Sci. 2025, 26(12), 5663; https://doi.org/10.3390/ijms26125663 - 13 Jun 2025
Viewed by 468
Abstract
Matrix metalloproteinase-9 (MMP-9) and lipopolysaccharide (LPS) levels are known to be elevated in obesity and contribute to metabolic dysfunction. 2-(1′H-indole-3′-carbonyl)-thiazole-4-carboxylic acid methyl ester (ITE), an endogenous ligand of the aryl hydrocarbon receptor (AhR), has been implicated in the regulation of inflammatory responses. This [...] Read more.
Matrix metalloproteinase-9 (MMP-9) and lipopolysaccharide (LPS) levels are known to be elevated in obesity and contribute to metabolic dysfunction. 2-(1′H-indole-3′-carbonyl)-thiazole-4-carboxylic acid methyl ester (ITE), an endogenous ligand of the aryl hydrocarbon receptor (AhR), has been implicated in the regulation of inflammatory responses. This study aimed to determine whether ITE can inhibit LPS-induced MMP-9 expression in monocytic cells and to explore the underlying signaling mechanisms involved. Human monocytic THP-1 cells and primary human monocytes were treated with LPS in the presence or absence of ITE. MMP-9 mRNA and protein levels were assessed using quantitative real-time PCR and ELISA, respectively, while gelatin zymography was employed to evaluate MMP-9 enzymatic activity. Chromatin immunoprecipitation followed by qPCR (ChIP-qPCR) was performed to assess NF-κB and AP-1 binding to the MMP-9 promoter region. Our findings demonstrate that ITE significantly suppresses LPS-induced MMP-9 gene and protein expression. This suppression is associated with a marked reduction in LPS-induced NF-κB and AP-1 transcriptional activity. ChIP-qPCR confirmed that ITE attenuates the recruitment of NF-κB and AP-1 to the MMP-9 promoter, thereby inhibiting its transcription. In summary, ITE downregulates LPS-induced MMP-9 expression by interfering with NF-κB/AP-1 signaling, suggesting a potential anti-inflammatory mechanism that could be relevant in the context of MMP-9-driven inflammatory conditions. Full article
(This article belongs to the Section Molecular Endocrinology and Metabolism)
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18 pages, 3065 KiB  
Article
Histone H3 Lysine 9 Acetylation Plays a Role in Adipogenesis of Periodontal Ligament-Derived Stem Cells
by Julio A. Montero-Del-Toro, Angelica A. Serralta-Interian, Geovanny I. Nic-Can, Mónica Lamas, Rodrigo A. Rivera-Solís and Beatriz A. Rodas-Junco
Epigenomes 2025, 9(2), 15; https://doi.org/10.3390/epigenomes9020015 - 24 May 2025
Viewed by 608
Abstract
Background: The epigenetic regulation of adipogenic differentiation in dental stem cells (DSCs) remains poorly understood, as research has prioritized osteogenic differentiation for dental applications. However, elucidating these mechanisms could enable novel regenerative strategies for soft tissue engineering. Periodontal ligament stem cells (PDLSCs) exhibit [...] Read more.
Background: The epigenetic regulation of adipogenic differentiation in dental stem cells (DSCs) remains poorly understood, as research has prioritized osteogenic differentiation for dental applications. However, elucidating these mechanisms could enable novel regenerative strategies for soft tissue engineering. Periodontal ligament stem cells (PDLSCs) exhibit notable adipogenic potential, possibly linked to histone 3 acetylation at lysine 9 (H3K9ac); however, the mechanistic role of this modification remains unclear. Methods: To address this gap, we investigated how histone deacetylase inhibitors (HDACis)—valproic acid (VPA, 8 mM) and trichostatin A (TSA, 100 nM)—modulate H3K9ac dynamics, adipogenic gene expression (C/EBPβ and PPARγ-2), and chromatin remodeling during PDLSCs differentiation. Techniques used included quantitative PCR (qPCR), lipid droplet analysis, and chromatin immunoprecipitation followed by qPCR (ChIP-qPCR). Results: TSA-treated cells exhibited increased lipid deposition with smaller lipid droplets compared to VPA-treated cells. Global H3K9ac levels correlated positively with adipogenic progression. VPA induced early upregulation of C/EBPβ and PPARγ-2 (day 7), whereas TSA triggered a delayed but stronger PPARγ-2 expression. ChIP-qPCR analysis revealed significant H3K9ac enrichment at the PPARγ-2 promoter in TSA-treated cells, indicating enhanced chromatin accessibility. Conclusions: These findings demonstrate that H3K9ac-mediated epigenetic remodeling plays a critical role in the adipogenic differentiation of PDLSCs and identifies TSA as a potential tool for modulating this process. Full article
(This article belongs to the Collection Epigenetic Regulation of Cellular Differentiation)
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19 pages, 3205 KiB  
Article
MSTN Regulates Bovine Skeletal Muscle Satellite Cell Differentiation via PSMA6-Mediated AKT Signaling Pathway
by Tengxia Ma, Meiling Miao, Xiangquan Liu, Linlin Zhang, Yiwen Guo, Xin Li, Xiangbin Ding, Hong Guo and Debao Hu
Int. J. Mol. Sci. 2025, 26(11), 4963; https://doi.org/10.3390/ijms26114963 - 22 May 2025
Viewed by 824
Abstract
MSTN has been used as a candidate gene in the genetics, breeding, and improvement of animal breeds. However, the possible mechanism by which the MSTN gene regulates muscle development through PSMA6 is not well understood. Previous methylome and transcriptome sequencing analyses of gluteal [...] Read more.
MSTN has been used as a candidate gene in the genetics, breeding, and improvement of animal breeds. However, the possible mechanism by which the MSTN gene regulates muscle development through PSMA6 is not well understood. Previous methylome and transcriptome sequencing analyses of gluteal muscle tissues from MSTN+/−Luxi cattle and wild-type Luxi cattle identified that the PSMA6 gene exhibited a negative correlation between methylation levels and transcriptional activity. To investigate whether MSTN expression regulates PSMA6 gene expression, we examined the effects of MSTN on DNA methyltransferases (DNMT1, DNMT2, DNMT3A, and DNMT3B) and DNA demethylases (TET1, TET2, and TET3). Additionally, chromatin immunoprecipitation (ChIP) assays were performed to detect the binding interaction between PSMA6 and TET2. In this paper, we first established an MSTN knockdown cellular model to preliminarily validate its regulatory effect on PSMA6 expression. Subsequently, the developmental impact of PSMA6 on bovine skeletal muscle satellite cells was further investigated through both knockdown and overexpression of the PSMA6 gene. Furthermore, we examined changes in the expression of key components of the AKT/mTOR signaling pathway to elucidate the mechanisms underlying the PSMA6-mediated regulation of satellite cell development. The results demonstrate that myostatin (MSTN) inhibition significantly decreased proteasome 20S subunit alpha-6 (PSMA6) gene expression, while increasing demethylase expression, particularly ten-eleven translocation-2 (TET2), which exhibited the most pronounced changes. During the cell proliferation stage, the markers Paired Box 7 (PAX7) and Ki-67 exhibited no significant changes, whereas the PSMA6 gene was either overexpressed or disrupted. Conversely, PSMA6 overexpression altered the myogenic differentiation markers, causing the differential regulation of myosin heavy chain (MyHC) and myogenin (MyoG) expression, with MyHC upregulation and concurrent MyoG downregulation. PSMA6 gene overexpression led to the downregulation of AKT1 and Rac1, as well as the activation of the AKT/mTOR pathway, including key factors such as mTOR, p-mTOR, RPS6, p-RPS6, and RhoA. PSMA6 interference resulted in the downregulation of p-mTOR and the upregulation of p-RPS6. Gene expression profiling in our study revealed that the myostatin (MSTN) knockout model significantly reduced the transcriptional levels of the proteasome α6 subunit (PSMA6) (p < 0.05), with the regulatory intensity showing a significant negative correlation with MSTN expression. This molecular evidence substantiates a negative regulatory axis between MSTN and PSMA6. Functional experiments demonstrated that PSMA6 overexpression specifically enhanced myotube formation rates in bovine skeletal muscle satellite cells, whereas siRNA-mediated PSMA6 knockdown exhibited no significant effects on cellular proliferation, indicating the functional specificity of this gene in myogenic differentiation. Mechanistic investigations further revealed that PSMA6 activates the canonical AKT/mTOR signaling transduction cascade through the phosphorylation of AKT and its downstream effector mTOR, thereby mediating the expression of myogenic regulatory factors MyoD and myogenin. Collectively, these findings demonstrate that MSTN deficiency alleviates the transcriptional repression of PSMA6, remodels skeletal muscle differentiation-associated signaling networks, and ultimately drives the directional differentiation of satellite cells toward myofiber specification. Full article
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17 pages, 1702 KiB  
Article
Inorganic Arsenic Induces Elevated p53 Levels with Altered Functionality Impacting the Expression of Toll-like Receptor 3 and Other Target Genes in Immortalized Prostate Epithelial Cells
by Nancy C. Pacheco-Castillo, Jesús Gómez-Montalvo, Vanesa Olivares-Illana, Félix Recillas-Targa, Erik J. Tokar, S. Eréndira Avendaño-Vázquez and Claudia Escudero-Lourdes
Int. J. Mol. Sci. 2025, 26(9), 4253; https://doi.org/10.3390/ijms26094253 - 29 Apr 2025
Viewed by 768
Abstract
Prostate cancer (PCa) is a major global health concern, particularly in advanced stages where chemotherapy resistance and androgen-independent tumor growth reduce survival rates to below 30%. Toll-like receptor 3 (TLR3), regulated by tumor suppressor p53, is a promising therapeutic target due to its [...] Read more.
Prostate cancer (PCa) is a major global health concern, particularly in advanced stages where chemotherapy resistance and androgen-independent tumor growth reduce survival rates to below 30%. Toll-like receptor 3 (TLR3), regulated by tumor suppressor p53, is a promising therapeutic target due to its role in tumor cell apoptosis. However, chronic exposure to inorganic arsenic (iAs), a known carcinogen, has been linked to PCa progression and reduced TLR3 expression and activation by polyinosinic/polycytidylic acid (Poly(I/C)), a synthetic ligand used in PCa immunotherapy. Here, we demonstrate that chronic sodium arsenite (NaAsO) exposure increases p53 transcript and protein levels in immortalized prostate epithelial cells. Despite this, key p53 target genes, including TLR3, CDKN1A, and BAX, were significantly downregulated, indicating a transcriptionally inactive p53. Chromatin immunoprecipitation (ChIP) confirmed diminished p53 binding to TLR3 and CDKN1A promoters, while sequencing ruled out TP53 mutations. A bioinformatic analysis revealed elevated TP53 but reduced TLR3 and CDKN1A in prostate adenocarcinoma, suggesting that iAs-induced oxidative stress disrupts p53 function. These findings reveal a novel mechanism by which iAs promotes PCa progression through impaired p53 activity, highlighting the need to explore post-translational and epigenetic factors affecting p53. Restoring p53 transcriptional activity may offer a therapeutic strategy for PCa patients exposed to NaAsO. Full article
(This article belongs to the Section Molecular Biology)
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24 pages, 4722 KiB  
Article
Bromodomain and Extra-Terminal Family Proteins BRD2, BRD3, and BRD4 Contribute to H19-Dependent Transcriptional Regulation of Cell Adhesion Molecules, Modulating Metastatic Dissemination Program in Prostate Cancer
by Valeria Pecci, Melissa Borsa, Aurora Aiello, Sara De Martino, Luca Cis, Cristian Ripoli, Dante Rotili, Francesco Pierconti, Francesco Pinto, Claudio Grassi, Carlo Gaetano, Antonella Farsetti and Simona Nanni
Non-Coding RNA 2025, 11(3), 33; https://doi.org/10.3390/ncrna11030033 - 29 Apr 2025
Viewed by 849
Abstract
Background/Objectives: Metastatic prostate cancer (PCa) remains a major clinical challenge with limited therapeutic options. The long non-coding RNA H19 has been implicated in regulating cell adhesion molecules and collective migration, key features of metastatic dissemination. This study investigates the role of the Bromodomain [...] Read more.
Background/Objectives: Metastatic prostate cancer (PCa) remains a major clinical challenge with limited therapeutic options. The long non-coding RNA H19 has been implicated in regulating cell adhesion molecules and collective migration, key features of metastatic dissemination. This study investigates the role of the Bromodomain and Extra-Terminal (BET) proteins BRD2, BRD3, and BRD4 in the H19-dependent transcriptional regulation of cell adhesion molecules. Currently, the major effects of BET inhibitors require androgen receptor (AR) expression. Methods: H19 was stably silenced in PC-3 (AR-null) and 22Rv1 (AR-positive) castration-resistant PCa cells. The cells were treated with the pan-BET inhibitors JQ1 and OTX015 or the BET degrader dBET6. In vivo, the effects of JQ1 were evaluated in xenograft mouse models. Chromatin immunoprecipitation (ChIP) and RNA-ChIP were used to assess BET protein recruitment and interaction with cell adhesion gene loci and H19. Organotypic slice cultures (OSCs) from fresh PCa surgical specimens were used as ex vivo models to validate transcriptional changes and BRD4 recruitment. Results: BET inhibition significantly reduced the expression of β4 integrin and E-cadherin and cell proliferation in both basal conditions, and following H19 knockdown in PC-3 and 22Rv1 cells. These effects were mirrored in JQ1-treated tumor xenografts, which showed marker downregulation and tumor regression. ChIP assays revealed that BRD4, more than BRD2/3, was enriched on β4 integrin and E-cadherin promoters, especially in regions marked by H3K27ac. H19 silencing markedly enhanced BRD4 promoter occupancy. RNA-ChIP confirmed a specific interaction between BRD4 and H19. These findings were validated in OSCs, reinforcing their clinical relevance. Conclusions: Our study demonstrates that BRD4 epigenetically regulates the H19-mediated transcriptional control of adhesion molecules involved in collective migration and metastatic dissemination. Importantly, these effects are independent of AR status, suggesting that targeting the H19/BRD4 axis may represent a promising therapeutic avenue for advanced PCa. Full article
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16 pages, 6755 KiB  
Article
Investigating the Associations Between Hmga2 Overexpression, R-Loop Reduction, and Bone Loss in Aging Mice
by Yangyang Cao, Yantong Wang and Dengsheng Xia
Medicina 2025, 61(5), 820; https://doi.org/10.3390/medicina61050820 - 29 Apr 2025
Viewed by 530
Abstract
Background and Objectives: Aging-related bone loss still lacks interventions. As bone marrow-derived mesenchymal stem cells (BMSCs) undergo aging, R-loop-induced DNA replication stress impairs the osteogenic ability of BMSCs. High-mobility group A-2 (Hmga2) acts as a DNA-binding protein, and the understanding of its underlying [...] Read more.
Background and Objectives: Aging-related bone loss still lacks interventions. As bone marrow-derived mesenchymal stem cells (BMSCs) undergo aging, R-loop-induced DNA replication stress impairs the osteogenic ability of BMSCs. High-mobility group A-2 (Hmga2) acts as a DNA-binding protein, and the understanding of its underlying mechanisms is crucial for developing effective preventive and therapeutic strategies. Materials and Methods: Aging mice were used as the experimental model, and mouse BMSCs were isolated from their femurs. Hmga2 was achieved through specific gene delivery methods. R-loop formation was detected using dot blotting, chromatin immunoprecipitation (ChIP), and DNA–RNA immunoprecipitation (DRIP) assays. Osteogenic differentiation was evaluated. Results: R-loops were highly accumulated in aging BMSCs. Notably, the key regulator Hmga2 reversed the accumulation of R-loops in aging BMSCs. Hmga2 overexpression significantly decreased the senescence and improved the osteogenic differentiation of aging mBMSCs. Mechanistically, R-loop-forming sequence (RLFS) regions were confirmed in key osteogenesis-related genes, including runt-related transcription factor 2 (Runx2). Hmga2 bound to the RLFS region of Runx2 and promoted its expression by reducing the R-loop level. More, Hmga2 treatment delivered via the AAV system effectively decreased bone loss in aging mice and increased the serum bone turnover biomarkers and collagen remodeling. Conclusions: Our study demonstrates that Hmga2 acts as an activator of aging BMSCs, significantly promoting their osteogenic ability by eliminating the aging-induced DNA replication stress caused by R-loops. Our findings provide new insights into the mechanisms of aging-related bone loss, suggesting that Hmga2 may be a new strategy for alleviating the bone loss phenotype in aging individuals. Full article
(This article belongs to the Section Genetics and Molecular Medicine)
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25 pages, 16893 KiB  
Article
IRF5 Mediates Artery Inflammation in Salt-Sensitive Hypertension by Regulating STAT1 and STAT2 Phosphorylation to Increase ESM1 Transcription: Insights from Bioinformatics and Mechanistic Analysis
by Qiaoyu Shao, Hao Wang, Shicheng Li, Mengying Zeng, Shuyang Zhang and Xiaowei Yan
Int. J. Mol. Sci. 2025, 26(8), 3722; https://doi.org/10.3390/ijms26083722 - 15 Apr 2025
Viewed by 756
Abstract
Salt-sensitive hypertension (SSH) is closely associated with arterial inflammation, yet its molecular mechanisms remain unclear. In this study, we utilized deoxycorticosterone acetate (DOCA)-salt-induced hypertensive mice, which exhibited elevated blood pressure and significant arterial inflammation. Single-cell RNA sequencing (scRNA-seq) identified interferon regulatory factor 5 [...] Read more.
Salt-sensitive hypertension (SSH) is closely associated with arterial inflammation, yet its molecular mechanisms remain unclear. In this study, we utilized deoxycorticosterone acetate (DOCA)-salt-induced hypertensive mice, which exhibited elevated blood pressure and significant arterial inflammation. Single-cell RNA sequencing (scRNA-seq) identified interferon regulatory factor 5 (IRF5) and its downstream targets, signal transducer and activator of transcription (STAT), as key regulators of these inflammatory changes. In vivo, IRF5 levels were significantly elevated in the DOCA group, while STAT1 and STAT2 protein levels were comparable to those in the normal salt group. However, nuclear levels of phosphorylated STAT1 (pSTAT1) and phosphorylated STAT2 (pSTAT2) were markedly higher in the DOCA group. Furthermore, scRNA-seq analysis showed increased IRF5 expression in endothelial cells (ECs) in both human and mouse aorta samples. In vitro, IRF5 knockdown in artery ECs led to a reduction in nuclear pSTAT1 and pSTAT2 expression. These results suggest that IRF5 promotes STAT1 and STAT2 phosphorylation, enabling their nuclear translocation. Additionally, RNA sequencing indicated a positive correlation between endothelial cell-specific molecule 1 (ESM1) and STAT1/STAT2. Using the UCSC and JASPAR databases, we identified multiple binding sites for the STAT1::STAT2 dimer on the ESM1 promoter. Luciferase reporter assays revealed enhanced ESM1 transcription following pSTAT1::pSTAT2 binding, and pinpoint potential binding sites. Chromatin Immunoprecipitation Quantitative PCR (ChIP-qPCR) further confirmed the specific binding sites between the pSTAT1::pSTAT2 dimer and the ESM1 promoter. These findings highlight the critical role of the IRF5-pSTAT1::pSTAT2-ESM1 pathway in the pathogenesis of SSH and suggest potential therapeutic targets. Full article
(This article belongs to the Section Molecular Informatics)
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13 pages, 2236 KiB  
Article
Berberine Suppression of Human IgE but Not IgG Production via Inhibition of STAT6 Binding Activity at IgE Promoter by BCL6
by Anish R. Maskey, Michelle Carnazza, Madison Spears, Steven Hemmindinger, Daniel Kopulos, Nan Yang, Humayun K. Islam, Augustine L. Moscatello, Jan Geliebter, Raj K. Tiwari and Xiu-Min Li
Cells 2025, 14(8), 591; https://doi.org/10.3390/cells14080591 - 14 Apr 2025
Cited by 1 | Viewed by 761
Abstract
IgE may lead to life-threatening anaphylaxis. Currently, no satisfactory treatment to inhibit IgE production exists. This study aims to explore the anti-IgE effect of berberine (BBR) and possible mechanisms using human tonsil cells. Tonsil cells were treated with BBR at different doses following [...] Read more.
IgE may lead to life-threatening anaphylaxis. Currently, no satisfactory treatment to inhibit IgE production exists. This study aims to explore the anti-IgE effect of berberine (BBR) and possible mechanisms using human tonsil cells. Tonsil cells were treated with BBR at different doses following stimulation with anti-CD40/IL4 alone or in combination with poly I:C and Pam3CSK4 for 10 or 4 days. IgE and IgG levels were determined by ELISA and cell viability by trypan blue exclusion. Gene expression was analyzed by qRT-PCR and affinity binding assay was performed by chromatin immunoprecipitation assay (ChIP). BBR showed dose-dependent inhibition of IgE production following anti-CD40/IL4 stimulation without affecting cell viability and IgG levels. BBR (10 µg/mL) completely inhibited IgE production by B cells stimulated with anti-CD40/IL4 in combination with vaccine adjuvants—poly I:C and Pam3CSK4 without affecting IgG levels and cell viability. BBR inhibited IgE heavy chain (IgEh), epsilon germline-transcript (εGLT), STAT6, and NFκB1 and enhanced IFN-γ, NFκB1A, and BCL6 gene expression. ChIP assay showed that BBR inhibited STAT6 binding in the IgEh promoter region by enhancing BCL6 binding. This study shows BBR regulates IgE in human tonsil cells by inhibiting STAT6 binding through BCL6 at the IgEh promoter showing its potential for treating IgE-mediated allergies. Full article
(This article belongs to the Section Cellular Immunology)
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16 pages, 1831 KiB  
Article
Overexpression of the Transcription Factor GmbZIP60 Increases Salt and Drought Tolerance in Soybean (Glycine max)
by Mengnan Chai, Fan Yang, Shuping Cai, Tingyu Liu, Xiaoyuan Xu, Youmei Huang, Xinpeng Xi, Jiahong Yang, Zhuangyuan Cao, Ling Sun, Danlin Dou, Xunlian Fang, Maokai Yan and Hanyang Cai
Int. J. Mol. Sci. 2025, 26(7), 3455; https://doi.org/10.3390/ijms26073455 - 7 Apr 2025
Cited by 1 | Viewed by 823
Abstract
The regulation of downstream responsive genes by transcription factors (TFs) is a critical step in the stress response system of plants. While bZIP transcription factors are known to play important roles in stress reactions, their functional characterization in soybeans remains limited. Here, we [...] Read more.
The regulation of downstream responsive genes by transcription factors (TFs) is a critical step in the stress response system of plants. While bZIP transcription factors are known to play important roles in stress reactions, their functional characterization in soybeans remains limited. Here, we identified a soybean bZIP gene, GmbZIP60, which encodes a protein containing a typical bZIP domain with a basic region and a leucine zipper region. Subcellular localization studies confirmed that GmbZIP60 is localized in the nucleus. Expression analysis demonstrated that GmbZIP60 is induced by salt stress, drought stress, and various plant hormone treatments, including abscisic acid (ABA), ethylene (ETH), and methyl jasmonate acid (MeJA). Overexpressing GmbZIP60 (OE-GmbZIP60) in transgenic soybean and rice enhanced tolerance to both salt and drought stresses. Quantitative real-time polymerase chain reaction (qRT-PCR) analysis indicated that the expression levels of abiotic stress-responsive genes were significantly higher in transgenic plants than in wild-type (WT) plants under stress conditions. Chromatin immunoprecipitation-qPCR (ChIP-qPCR) analysis further confirmed that GmbZIP60 directly binds to the promoters of abiotic stress-related genes induced by ABA, ETH, JA, and salicylic acid (SA). Overall, these findings revealed GmbZIP60 as a positive regulator of salt and drought stress tolerance. Full article
(This article belongs to the Special Issue Plant Response to Drought, Heat, and Light Stress)
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11 pages, 5284 KiB  
Article
DNA Sequence Changes Resulting from Codon Optimization Affect Gene Expression in Pichia pastoris by Altering Chromatin Accessibility
by Chaoyu Lu, Linna Guo, Bohao Fang, Jiacheng Shi and Mian Zhou
J. Fungi 2025, 11(4), 282; https://doi.org/10.3390/jof11040282 - 3 Apr 2025
Viewed by 817
Abstract
Codon optimization is a widely employed strategy to enhance protein expression. However, it occasionally leads to unexpected transcriptional repression despite preserving amino acid sequences. This study investigates the mechanistic basis of such transcriptional attenuation by analyzing two gene candidates (0432 and Fluc [...] Read more.
Codon optimization is a widely employed strategy to enhance protein expression. However, it occasionally leads to unexpected transcriptional repression despite preserving amino acid sequences. This study investigates the mechanistic basis of such transcriptional attenuation by analyzing two gene candidates (0432 and Fluc) in the common expression chassis P. pastoris. Both genes experienced severe mRNA reduction following codon optimization. Evidenced by histone H3 chromatin immunoprecipitation (ChIP) and a DNase I hypersensitivity assay, gene sequences with transcriptional repression displayed elevated nucleosome occupancy and reduced chromatin accessibility. The above change was caused by an ORF sequence change independent of the promoter, since transcriptional attenuation and compromised chromatin accessibility were still observed after replacing the strong promoter PGAP with Ppor1 or Prps8b. Our findings challenge the conventional view of codon optimization as solely translation-centric, revealing its capacity to preemptively modulate transcription through chromatin accessibility. This work underscores the necessity of integrating chromatin-level considerations into synthetic gene design to avoid unintended transcriptional silencing and optimize expression outcomes. Full article
(This article belongs to the Section Fungal Genomics, Genetics and Molecular Biology)
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23 pages, 2980 KiB  
Article
H2AJ Is a Direct Androgen Receptor Target Gene That Regulates Androgen-Induced Cellular Senescence and Inhibits Mesenchymal Markers in Prostate Cancer Cells
by Mehdi Heidari Horestani, Golnaz Atri Roozbahani and Aria Baniahmad
Cancers 2025, 17(5), 791; https://doi.org/10.3390/cancers17050791 - 25 Feb 2025
Viewed by 1124
Abstract
Background: Prostate cancer (PCa) is a significant public health issue, particularly in developed countries. The androgen receptor (AR) plays a key role in regulating both the normal development and the proliferation of PCa. Bipolar androgen therapy, which involves treatment with supraphysiological androgen levels [...] Read more.
Background: Prostate cancer (PCa) is a significant public health issue, particularly in developed countries. The androgen receptor (AR) plays a key role in regulating both the normal development and the proliferation of PCa. Bipolar androgen therapy, which involves treatment with supraphysiological androgen levels (SALs), has been shown to inhibit PCa growth. SAL induces cellular senescence in AR-positive PCa cell lines, human tumor samples, and xenografted mouse models. Methods: Transcriptome and chromatin immunoprecipitation (ChIP)-seq analysis, ChIP-qPCR, knockdown (KD), overexpression (OE), qRT-PCR, immunodetection, in situ histochemistry. Results: Here, we show using ChIP-seq and RNA-seq that H2AJ, a variant of the canonical histone H2A, is a direct target gene of AR that regulates cellular senescence and the formation of senescence-associated heterochromatin foci (SAHF). Accordingly, bioinformatic analyses reveal a large overlap of the H2AJ transcriptome with the cellular senescence score of PCa. Analyzing a large cohort of patient samples, the expression of H2AJ is higher in tumor samples compared to normal samples suggesting growth-promoting activity. Interestingly, however, the expression is diminished in metastatic tumor samples, indicating that H2AJ inhibits the mesenchymal transition in PCa cells. Functionally, the KD of H2AJ inhibits growth, whereas the H2AJ overexpression promotes cell growth. Furthermore, these data suggest that H2AJ inhibits the expression of mesenchymal markers, in agreement with the low expression of H2AJ in metastatic forms of tumors from patient cohorts. Conclusion:H2AJ is a direct positively AR-regulated target gene induced by SALs that regulates cellular senescence, promotes growth, and inhibits the expression of mesenchymal markers. Full article
(This article belongs to the Section Molecular Cancer Biology)
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Article
Rocaglamide Suppresses Allergic Reactions by Regulating IL-4 Receptor Signaling
by Hyein Jo, Misun Kim, Jaewhoon Jeoung, Wonho Kim, Yoon Ho Park, Hyun Suk Jung, Wook Lee and Dooil Jeoung
Molecules 2025, 30(4), 840; https://doi.org/10.3390/molecules30040840 - 11 Feb 2025
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Abstract
Rocaglamide (Roc-A), a natural phytochemical isolated from Aglaia species, is known to exert anticancer effects. Allergic inflammation can enhance the tumorigenic potential of cancer cells. We hypothesized that Roc-A could regulate allergic inflammation. Roc-A prevented an antigen from increasing the hallmarks of allergic [...] Read more.
Rocaglamide (Roc-A), a natural phytochemical isolated from Aglaia species, is known to exert anticancer effects. Allergic inflammation can enhance the tumorigenic potential of cancer cells. We hypothesized that Roc-A could regulate allergic inflammation. Roc-A prevented an antigen from increasing the hallmarks of allergic reactions in vitro. Roc-A suppressed passive cutaneous anaphylaxis (PCA) and passive systemic anaphylaxis (PSA). RNA sequencing analysis showed that Roc-A prevented the antigen from increasing the expression of IL-4 in RBL2H3 cells. Roc-A also prevented the antigen from increasing the expression of interleukin-4 receptor (IL-4R). Roc-A was found to form a hydrogen-bonding network with residues N92 and L64 of IL-4R in a molecular docking simulation. Roc-A prevented the antigen from inducing the binding of IL-4R to JAK1. Chromatin immunoprecipitation (ChIP) assays showed that C-Jun could bind to promoter sequences of IL-4 and IL-4R. Mouse recombinant IL-4 protein increased β-hexosaminidase activity, IL-4R expression, and the hallmarks of allergic inflammation in the antigen-independent manner. Mouse recombinant IL-4 protein increased the expressions of CD163 and arghinase-1 and markers of M2 macrophages, but decreased the expression of iNOS, a marker of M1 macrophages in lung macrophages. Roc-A regulated the effects of a culture medium of antigen-stimulated RBL2H3 cells on the expressions of iNOS and arginase-1 in RAW264.7 macrophages. The blocking of IL-4 or downregulation of IL-4R exerted negative effects on the hallmarks of allergic reactions in vitro. The blocking of IL-4 or downregulation of IL-4R also exerted negative effects on PCA, and the downregulation of IL-4R exerted negative effects on PSA. An miR-34a mimic exerted negative effects on allergic reactions in vitro. The downregulation of IL-4R prevented the antigen from decreasing the expression of miR-34a in RBL2H3 cells. We identified chemicals that could bind to IL-4R via molecular docking analysis. The IL-4R docking chemical 1536801 prevented the antigen from increasing β-hexosaminidase activity and the hallmarks of allergic reactions. The IL-4R docking chemical 1536801 also exerted a negative effect on PCA. TargetScan analysis predicted miR-34a as a negative regulator of IL-4R. We found that the anti-allergic effect of Roc-A and its mechanisms were associated with miR-34a. Taken together, our results show that understanding IL-4R-mediated allergic reactions can provide clues for the development of anti-allergy therapeutics. Full article
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