Search Results (181)

The dynamic remodeling of the fungal cell wall depends on a balance between chitin synthesis and degradation. Chitinases are critical for nutrient acquisition, cell wall remodeling, and defense; yet, the upstream regulatory mechanisms controlling chitinase gene expression remain poorly understood. Here, Tandem Affinity Purification–Mass Spectrometry (TAP–MS) with the Penicillium oxalicum Snf1 kinase (PoSnf1) as bait identified the zinc finger transcription factor (TF) PoCon7 as a putative target of the Snf1 kinase complex. This complex comprises the catalytic α subunit Snf1, one of three alternative β subunits Gal83, and the γ subunit Snf4. Although PoCon7 does not directly bind PoSnf1 or PoSnf4, it specifically interacts with PoGal83. Phylogenetic analysis indicates that PoCon7 is a conserved, nuclear-localized C2H2-type TF in filamentous fungi. PoCon7 is likely essential for fungal viability, as only a truncated mutant (con7-B) could be generated, while full deletion was lethal. The con7-B mutant displayed delayed hyphal extension, reduced conidiation, downregulation of developmental genes, and upregulation of cell wall-degrading enzyme (CWDE) genes. DNA Affinity Purification Sequencing (DAP-seq) revealed that PoCon7 binds target gene promoters via the motif 5′-TATTWTTAT-3′. ChIP-qPCR confirmed PoCon7 enrichment at specific sites within the chitinase genes chi18A and chi18C, and the disruption of PoCon7 markedly reduced their expression. Thus, PoCon7 represents the first TF shown to directly regulate chitinase gene expression in filamentous fungi. Full article

(1) Background: Epigenetic mechanisms play a significant role in plant architecture. Histone deacetylases, as crucial epigenetic regulators, shape plant architecture by modifying chromatin structure and regulating gene expression. (2) Methods: This study combined bioinformatic identification of BpHST1 with its functional characterization in transgenic birch overexpressing 35S::BpHST1::FLAG, including phenotypic and cytological analyses. The putative direct targets of BpHST1 were further identified by integrating RNA-seq and ChIP-seq data. (3) Results: Phylogenetic analysis revealed that the HST1 orthologs from birch and peach form a distinct clade, consistent with their high degree of protein sequence conservation. BpHST1 exhibited light-inducible and leaf-preferential expression, with transcript levels elevated under light versus dark conditions, enriched in leaves relative to roots, and promoter activity confirming this spatial patterning. Overexpression of BpHST1 significantly suppressed plant height, cell length, cell width, and photosynthetic capacity. Integrated RNA-seq and ChIP-seq analysis suggested that BpLHCA2 possible functions as a direct downstream target of BpHST1, mediating plant growth and development. (4) Conclusions: Our findings delineated the role of BpHST1 in regulating plant architecture through comprehensive expression and functional analyses, and identified a candidate target gene. This study provided a novel insight into the molecular mechanisms governing plant architecture and offers potential strategies for future epigenetic breeding. Full article

Organic anion transporting polypeptide 1B1 (OATP1B1) is specifically expressed at the basolateral membrane of human liver cells and transports a wide range of endogenous compounds, toxins, and drugs, making it a crucial factor in determining the pharmacokinetics of many clinically important medications. Triptergium wilfordii Hook. f. (TWHF) is a traditional Chinese medicine known for its long history of therapeutic effects. A previous study conducted in our laboratory found that major components of TWHF, including wilforine (WFR), wilforgine (WFG), celastrol (CL), and triptolide (TPL), directly suppressed the function of OATP1B1. In the current study, we investigated the long-term (24 h) effects of these TWHF components on the transporter. It was found that TPL was the most potent compound exhibiting inhibitory effects. Mechanistically, TPL accelerated the degradation of OATP1B1, which is likely mediated by serum and glucocorticoid-induced kinase 1 (SGK1). TPL downregulated the mRNA expression of SGK1 and reduced the nuclear accumulation of nuclear factor kappa B (NFκB). Further analysis of the upstream sequence of SGK1 identified three potential binding sites for NFκB. Both luciferase activity assays and chromatin immunoprecipitation (ChIP) analyses confirmed the binding of NFκB to two specific sites located at −1015 bp~−1006 bp and −319 bp~−310 bp. Full article

As reported in earlier work, when a pea apyrase, psNTP9 (PS), and a modified version of it, psNTP9-DM (DM), are expressed in Saccharomyces cerevisiae, they localize to nuclei, binding to largely non-overlapping promoter regions of chromatin. PS- and DM-expressing yeast also exhibit different expression profiles for potentially regulated target genes, consistent with observed phenotypes. In the present study, we use ChIP-seq assays to show that PS and DM also associate with largely different promoter regions of Arabidopsis genes, with similar non-overlapping expression profiles for potential target genes. Functional studies, using electrophoretic mobility shift assays (EMSA), verified PS-specific binding to yeast or plant promoter binding sites. DM binding to both heterologous dsDNA and to PS-specific binding site sequences was minimal. AlphaFold3 modeling of PS protein binding to a yeast PHM6 promoter sequence identified potential DNA-binding residues and a potential binding site motif (5′-(G/T)GG(G/T)A-3′) that is also present in two Arabidopsis promoter binding sites. These novel findings extend the previously known functions of PS and other plant apyrases in the Golgi or extracellular matrix, and support their potential function as DNA-binding proteins that can regulate gene expression in both yeast and Arabidopsis. Full article

Olanzapine and clozapine, two of the most efficacious second-generation antipsychotic drugs (SGAs), are known to cause serious metabolic side effects. Despite their clinical utility, the epigenetic basis of these metabolic side-effects remains poorly understood. This exploratory study investigated whether histone methylation is associated with metabolic disorders following chronic SGA treatment. Rats were treated with olanzapine or clozapine for 9 weeks and then sacrificed 2 h after the final treatment. After evaluating the metabolic parameters, Chromatin immunoprecipitation (ChIP)-deep sequencing was conducted on liver tissue pooled from twelve samples per group to quantify histone H3K4me2 methylation and transcriptional changes. Gene ontology term enrichment analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis were used to explore shared functional pathways of genes with differential histone methylation. Key findings revealed that both olanzapine and clozapine induced widespread changes in hepatic histone methylation, particularly hypermethylation at H3K4me2 across genes involved in lipid and glucose metabolism, insulin signalling, and adipogenesis. Olanzapine- and clozapine-treated rats displayed increased H3K4me2 levels at numerous gene loci and at distinct genomic regions. These findings suggest the importance of monitoring metabolic parameters in psychiatric patients and potential novel strategies to mitigate SGA-induced metabolic side effects. Full article

An emerging challenge in prostate cancer (PCa) treatment is the development of drug cross-resistance, wherein resistance to enzalutamide (ENZ), an androgen receptor signaling inhibitor (ARSI), also confers resistance to subsequent ARSI and docetaxel (DTX) treatments. The mechanisms underlying this drug cross-resistance remain unclear. Through RNA sequencing, we identified 93 overlapping differentially expressed genes (DEGs) in ENZ- and DTX-resistant PCa cells. Among the DEGs, HSPB1, which encodes heat shock protein 27 (HSP27), emerged as a key gene of interest. HSP27 is a known target of lens epithelium-derived growth factor p75 (LEDGF/p75), a transcription coactivator regulated by glucocorticoid receptor (GR). Both GR and LEDGF/p75 are overexpressed in advanced PCa and promote drug resistance. HSP27 was overexpressed in ENZ and DTX cross-resistant PCa cell lines and its expression was decreased upon GR or LEDGF/p75 silencing. ChIP sequencing confirmed GR binding at the HSPB1 promoter. Pharmacological targeting of HSP27 in drug-resistant cells reduced proliferation, clonogenicity, and tumorsphere formation, and restored sensitivity to ENZ and DTX. Notably, high transcript expression of a GR-LEDGF/p75-HSP27 gene panel correlated with worse overall survival in PCa patients (n = 4259). These findings identified this axis as a driver of PCa drug cross-resistance and promising therapeutic target for overcoming treatment failure. Full article

The submandibular glands (SMGs), along with the parotid and sublingual glands, generate the majority of saliva and play critical roles in maintaining oral and systemic health. Despite their physiological importance, long-term therapeutic options for salivary gland dysfunction remain limited, highlighting the need for a deeper molecular understanding of SMG biology, particularly in humans. To address this knowledge gap, we have performed transcriptomic- and epigenomic-based analyses and molecular characterization of the human SMG. Our integrated analysis of multiorgan RNA-sequencing datasets has identified an SMG-enriched gene expression signature comprising 289 protein-coding and 75 long non-coding RNA (lncRNA) genes that include both known regulators of salivary gland function and several novel candidates ripe for future exploration. To complement these transcriptomic studies, we have generated chromatin immunoprecipitation sequencing (ChIP-seq) datasets of key histone modifications on human SMGs. Our epigenomic analyses have allowed us to identify genome-wide enhancers and super-enhancers that are likely to drive genes and regulatory pathways that are important in human SMG biology. Finally, comparative analysis with mouse and human SMG and other tissue datasets reveals evolutionary conserved gene and regulatory networks, underscoring fundamental mechanisms of salivary gland biology. Collectively, this study offers a valuable knowledge-based resource that can facilitate targeted research on salivary gland dysfunction in human patients. Full article

G-quadruplex (G4) ChIP-Seq data are critical for studying the roles of G4 structures in various biological processes, yet their reproducibility remains systematically uncharacterized. In this study, we evaluated the consistency of in vivo G4 peaks across multiple replicates in three publicly available datasets. We observed considerable heterogeneity in peak calls, with only a minority of peaks shared across all replicates. To address this challenge, we compared three computational methods—IDR, MSPC, and ChIP-R—for assessing reproducibility and found that MSPC is the optimal solution in reconciling inconsistent signals in G4 ChIP-Seq data. We further demonstrated that employing at least three replicates significantly improved detection accuracy compared to conventional two-replicate designs, while four replicates proved sufficient to achieve reproducible outcomes, with diminishing returns beyond this number. Moreover, we showed that the reproducibility-aware analytical strategies can partially mitigate the adverse effects of low sequencing depth, though they do not fully substitute for high-quality data. Based on our findings, we recommend 10 million mapped reads as a minimum standard for G4 ChIP-Seq experiments, with 15 million or more reads being preferable for optimal results. Our study provides practical guidelines for experimental design and data analysis in G4 studies, emphasizing the importance of replication and robust bioinformatic strategies to enhance the reliability of genome-wide G4 mapping. Full article

Plants have evolved a complex, multilayered immune system that integrates molecular recognition, signaling pathways, epigenetic regulation, and small RNA-mediated control. Recent studies have shown that DNA-level regulatory mechanisms, such as RNA-directed DNA methylation (RdDM), histone modifications, and chromatin remodeling, are critical for modulating immune gene expression, allowing for rapid and accurate pathogen-defense responses. The epigenetic landscape not only maintains immunological homeostasis but also promotes stress-responsive transcription via stable chromatin modifications. These changes contribute to immunological priming, a process in which earlier exposure to pathogens or abiotic stress causes a heightened state of preparedness for future encounters. Small RNAs, including siRNAs, miRNAs, and phasiRNAs, are essential for gene silencing before and after transcription, fine-tuning immune responses, and inhibiting negative regulators. These RNA molecules interact closely with chromatin features, influencing histone acetylation/methylation (e.g., H3K4me3, H3K27me3) and guiding DNA methylation patterns. Epigenetically encoded immune memory can be stable across multiple generations, resulting in the transgenerational inheritance of stress resilience. Such memory effects have been observed in rice, tomato, maize, and Arabidopsis. This review summarizes new findings on short RNA biology, chromatin-level immunological control, and epigenetic memory in plant defense. Emerging technologies, such as ATAC-seq (Assay for Transposase-Accessible Chromatin using Sequencing), ChIP-seq (Chromatin Immunoprecipitation followed by Sequencing), bisulfite sequencing, and CRISPR/dCas9-based epigenome editing, are helping researchers comprehend these pathways. These developments hold an opportunity for establishing epigenetic breeding strategies that target the production of non-GMO, stress-resistant crops for sustainable agriculture. Full article

FOXL2 (forkhead box protein L2) is a transcription factor, its function and regulatory mechanism have been mainly studied in mammals; related research on marine invertebrates is still insufficient. It was found that oogenesis was affected, and even a small number of cells resembling spermatogonial morphology appeared in C. farreri ovaries after the FOXL2 was knocked down through RNA interference (RNAi) technology in our laboratory previously. Based on previous research, this paper conducted transcriptome sequencing and differential expression analysis on the ovarian tissues between the experimental group (post-RNAi) and the control group (pre-RNAi) of C. farreri, and used recombinant C. farreri FOXL2 protein for antibody production in Chromatin Immunoprecipitation Sequencing (ChIP seq) experiments to comprehensively analyze the pathways and key genes regulated by FOXL2 during oogenesis. The results showed that in the RNAi experimental group, 389 genes were upregulated, and 1615 genes were downregulated. Among the differentially expressed genes (DEGs), the differential genes related to gender or gonadal development are relatively concentrated in physiological processes such as steroid hormone synthesis, spermatogenesis, gonadal development, and ovarian function maintenance, as well as the FoxO and estrogen signaling pathways. Combining transcriptome and ChIP-seq data, it was found that there were some genes related to sex gonadal development among genes which were directly regulated by FOXL2, such as Wnt4, SIRT1, HSD17B8, GABABR1, KRAS, NOTCH1, HSD11B1, cPLA2, ADCY9, IP3R1, PLCB4, and Wnt1. This study lays the foundation for a deeper understanding of the FOXL2′s specific regulatory mechanism during oogenesis in scallops as a transcription factor. Full article

Background: Streptomyces bacteria are prolific producers of secondary metabolites (SMs), including many antibiotics. However, most biosynthetic gene clusters (BGCs) remain silent under laboratory conditions. Global transcriptional regulators, such as AdpA, can activate these BGCs, but their roles in secondary metabolism are not fully understood. This study investigates the regulatory function of AdpA in Streptomyces venezuelae (AdpA_Sv), a fast-growing model species and natural chloramphenicol producer that encodes over 30 BGCs. Methods: We applied RNA-seq and ChIP-seq at 12 and 20 h—corresponding to vegetative and aerial hyphae stages—to profile the AdpA_Sv regulatory network. Results: AdpA_Sv influenced the expression of approximately 3000 genes, including those involved in primary metabolism, quorum sensing, sulfur metabolism, ABC transporters, and all annotated BGCs, and it bound to around 200 genomic sites. Integration of RNA-seq and ChIP-seq data identified a core regulon of 49–91 directly regulated genes, with additional effects likely mediated indirectly via other transcription factors or non-canonical binding sites. Motif analysis confirmed similarity to the canonical Streptomyces griseus AdpA-binding sequence, with a novel 5-bp 3′ extension. AdpA_Sv directly regulated several SM pathways, including chloramphenicol biosynthesis, potentially alleviating Lsr2-mediated repression. Conclusions: This study defines, for the first time, the direct AdpA regulon in S. venezuelae and establishes AdpA_Sv as a central regulator of secondary metabolism. Our findings highlight S. venezuelae as a promising chassis strain for heterologous expression and suggest strategies for activating silent BGCs in other Streptomyces species. Full article

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

Nicotine-induced oxidative stress contributes significantly to vascular endothelial dysfunction. While negative air ions (NAIs) demonstrate potential blood-pressure-regulating and antioxidant properties, their mechanistic role remains unclear. This study examined the effects of NAIs against nicotine-induced oxidative damage and vascular endothelial injury in spontaneously hypertensive rats (SHRs). Western blotting was used to detect the expression levels of the α7nAChR/MAPK/AP1 pathway. Transcriptomic sequencing was performed to identify the differentially expressed genes after treatment with nicotine or NAIs. Furthermore, reactive oxygen species (ROS), endothelin-1 (ET-1), and [Ca²⁺]_i levels were detected in human aortic endothelial cells (HAECs) treated with nicotine, and the relationship between transcription factor activator protein 1 (AP1) and the target genes was further elucidated through ChIP–qPCR. Nicotine exposure in SHRs elevated blood pressure and induced oxidative damage through α7nAChR/MAPK/AP1 pathway activation, causing endothelial structural disruption. These effects manifested as decreased NO/eNOS and increased ET-1/ET_ab expression, while these changes were reversed by NAIs. In HAECs, nicotine impaired proliferation while increasing oxidative stress and [Ca²⁺]_i levels. This endothelial damage was markedly attenuated by either NAIs or fibronectin 1 (Fn1)/secreted phosphoprotein 1 (Spp1) knockdown. Mechanistically, we identified AP1 as the transcriptional regulator of FN1 and SPP1. NAIs attenuate nicotine-induced endothelial dysfunction in hypertension by inhibiting AP1-mediated FN1 and SPP1 activation, providing novel insights for smoking-associated cardiovascular risk. Full article

GCN5-containing SAGA complex is evolutionarily conserved across yeast, plants, and humans and acts as a general transcription coactivator in the genome-wide regulation of genes. In Plasmodium falciparum, PfGCN5 forms a divergent complex, and the mis-localization of this complex by deleting the PfGCN5 bromodomain (ΔBrd) causes a plethora of growth defects. To directly test the PfGCN5 function, we performed conditional knockdown (KD) of PfGCN5. Whereas PfGCN5 KD phenotypically recapitulated the ΔBrd growth defects, it caused fewer transcriptional alterations compared to ΔBrd. To decipher the mechanism by which PfGCN5 regulates gene expression, we applied a new chromatin landscape analysis tool, CUT&Tag-seq, to map the chromatin localization of PfGCN5 and its deposited histone mark H3K9ac. Compared to ChIP-seq, CUT&Tag-seq identified substantially more H3K9ac peaks in the promoters of its target genes, with the peak intensity positively correlated with the levels of gene expression. CUT&Tag-seq analysis was remarkably more sensitive in mapping chromatin positions of PfGCN5, which colocalized with H3K9ac. The genes enriched with PfGCN5/H3K9ac signals at their promoters are involved in broad biological processes. Notably, PfGCN5′s positions overlapped with sequence motifs recognized by multiple apetela2 (AP2)-domain-containing transcription factors (AP2 TFs), suggesting that they recruited PfGCN5 to these promoters. Additionally, PfGCN5 was also colocalized with AP2-LT, further validating that AP2-LT is an integral component of the PfGCN5 complex. Collectively, these findings establish PfGCN5 as a master gene regulator in controlling general and parasite-specific cellular processes in this low-branching parasitic protist. Full article

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