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Sphingobium lignivorans SYK-6 catabolizes guaiacylglycerol-β-guaiacyl ether (GGE, a β-O-4-type dimer) and 1,2-diguaiacylpropane-1,3-diol (DGPD, a β-1-type dimer) derived from lignin. Recently, SLG_35860 containing TetR- and MarR-type transcriptional regulator motifs was suggested to be involved in the regulation of GGE and DGPD catabolism. Here we investigated the role of SLG_35860 in the transcriptional regulation of GGE and DGPD catabolism genes. SLG_35860 designated ligS repressed 11 genes involved in GGE and DGPD catabolism. LigS binds directly to specific sequences in the promoter region of each gene. The MarR domain was shown to be involved in these bindings; however, GGE, DGPD, and their metabolites did not function as effectors of LigS. We discovered unidentified compound(s) in the black liquor of oxygen-soda anthraquinone pulping of Japanese cedar that SYK-6 cannot metabolize and that acted as effector(s). Therefore, LigS constantly represses the transcription of the GGE and DGPD catabolism genes to low levels. Based on these findings, we examined the productivity of a polymer building block, 2-pyrone-4,6-dicarboxylic acid (PDC), from GGE, DGPD, and a GGE metabolite using an engineered ligS mutant. The rates of PDC production from each compound by this strain were 1.5–6.0 times higher than those of a PDC-producing strain carrying ligS. [ABSTRACT FROM AUTHOR]

Pollutant-derived risks to human and environmental health are exacerbated by slow natural attenuation rates, often driven by pollutant toxicity to microorganisms that can degrade them or limitations to the ability of microorganisms to metabolise them. This review explores mechanisms employed by bacteria to protect themselves from pollutant toxicity in the context of the evolution of pollutant-degrading abilities. The role of promiscuous enzymes in pollutant transformation is subsequently reviewed, highlighting the emergence of novel metabolic pathways and their transcriptional regulation in response to pollutant exposure, followed by the gene transcription regulation to optimise the cellular component synthesis for adaptation on the novel substrate. Additionally, we discuss epistatic interactions among mutations vital for this process both at macromolecular and at cellular levels. Finally, evolutionary constraints towards enhanced fitness in the context of pollutant degradation are considered, the constraints imposed by the epistasis from mutations on both enzyme level and cellular level, concluding with challenges and emerging opportunities to develop sustainable contaminated site remediation technologies. Key points: •Pollutants can exert toxicity on cellular membrane, enzyme and gene transcription. •Bacteria can patch promiscuous enzymes into novel pathway to degrade pollutants. •The evolution trajectory is constrained by epistasis from mutations on enzyme and cellular level. [ABSTRACT FROM AUTHOR]

Aims: Autophagy is a protective mechanism of cardiomyocytes. Hyperhomocysteinemia (HHcy) elevates oxidative and nitrosative stress levels, leading to an abnormal increase in nitration protein, possibly leading to abnormal autophagy regulation in cardiomyocytes. However, the regulatory effect of HHcy on autophagy at the post-translational modification level is still unclear. Here, we aimed to explore the regulatory mechanism of HHcy on transcription factor EB (TFEB) and nitration of CCAAT/enhancer-binding protein beta (C/EBPβ), a transcriptional repressor of Tfeb, on autophagy in cardiomyocytes. Results: In this study, we established the HHcy rat model by feeding a 2.5% (w/w) methionine diet. The nitration level of C/EBPβ was increased in HHcy, which promoted the entry of C/EBPβ into the nucleus, enhanced the transcriptional suppressive effect of C/EBPβ on Tfeb, and induced insufficient autophagy in cardiomyocytes. Furthermore, we confirmed that the Tyr 274 site of C/EBPβ could undergo nitration induced by HHcy. Once C/EBPβ was nitrated on the Tyr 274 site, the nuclear translocation of C/EBPβ and transcription suppressor function of C/EBPβ on Tfeb were enhanced. Innovation and Conclusion: We find that C/EBPβ is a transcriptional repressor of Tfeb, and HHcy induces the nitration at the Tyr 274 site of C/EBPβ, leading to autophagic flux blockage in cardiomyocytes. These data indicated that nitrated C/EBPβ might be a potential therapeutic target against HHcy-induced autophagy insufficiency of cardiomyocytes. Antioxid. Redox Signal. 42, 165–183. [ABSTRACT FROM AUTHOR]

Background: In mammals, female fertility is influenced by the result of follicular development (ovulation or atresia). Follicular atresia is a complex physiological process that results in the degeneration of oocytes from the ovary. However, the molecular mechanisms of oocyte degeneration and key protein markers of follicular atresia remain unclear. In this study, we investigated the complex transcriptional regulatory mechanisms and protein profiles in oocytes and follicular fluid in atretic follicle stages using single-cell RNA sequencing and tandem mass tag proteomics. Results: First, through paired analysis of different follicle development stages, we identified 175 atresia-specific genes and eight candidate oocyte-secreted factors, including PKG1, YTHDF2, and MYC. Meanwhile, we also characterized unique features of the oocyte transcriptional landscape in the atretic follicle stage that displayed cell death-related transcriptional changes and mechanisms, such as autophagy (TBK1 and IRS4), necroptosis (PKR), and apoptosis (MARCKS). Moreover, we identified atresia-specific genes, namely FTH1, TF, and ACSL4, which may participate in regulation of oocyte ferroptosis in atretic follicles through a series of mechanisms including ferritinophagy, ferritin transport, and lipid metabolism. Additionally, we uncovered 333 differentially expressed proteins that may coordinate follicular atresia and revealed key pathways, such as negative regulation of angiogenesis, metabolic pathways, and transcription and mRNA splicing, that lead to oocyte degeneration. Finally, by combining transcriptome and proteomics analyses, we identified two oocyte-secreted biomarkers, PGK1 and ANGPT2, that may be associated with follicular atresia. Conclusions: In conclusion, our work offers a thorough characterization of oocyte transcription mechanism and follicular fluid protein changes in ovine atretic follicles, which offers a crucial reference for analyzing the mechanism of follicular atresia and establishing an oocyte quality assessment system in sheep. Highlights: 1. Distinct transcription regulation and protein profiles exist in healthy and atretic follicles. 2. Ferroptosis-induced oocyte degeneration occurs in atretic follicles. 3. Identification of oocyte-secreted biomarkers is associated with follicular atresia. [ABSTRACT FROM AUTHOR]

The protein complexes catalyzing the mono-, di-, and trimethylation and demethylation of H3 lysine 4 (H3K4), as well as those that read these modifications, are essential for differentiation and development. More specifically, trimethylated H3K4 (H3K4me3) plays critical roles in regulating gene expression, as well as transcriptional memory and consistency. Recent studies have indicated that the roles of H3K4me3 in gene expression may be different from what was originally thought. Somatic alterations in genes regulating the methylation and demethylation of H3K4 are common in cancer. Epigenetic modifications, including posttranslational modifications of histones, are closely linked to transcriptional regulation. Trimethylated H3 lysine 4 (H3K4me3) is one of the most studied histone modifications owing to its enrichment at the start sites of transcription and its association with gene expression and processes determining cell fate, development, and disease. In this review, we focus on recent studies that have yielded insights into how levels and patterns of H3K4me3 are regulated, how H3K4me3 contributes to the regulation of specific phases of transcription such as RNA polymerase II initiation, pause–release, heterogeneity, and consistency. The conclusion from these studies is that H3K4me3 by itself regulates gene expression and its precise regulation is essential for normal development and preventing disease. [ABSTRACT FROM AUTHOR]

Our previous single-cell RNA sequencing study in the adult human heart revealed that cardiomyocytes from both the atrium and ventricle display high activities of Krüppel-like factor 2 (KLF2) regulons. However, the role of the transcription factor KLF2 in cardiomyocyte biology remains largely unexplored. We employed transverse aortic constriction surgery in male C57BL/6 J mice to develop an in vivo model of cardiac hypertrophy, and generated different in vitro cardiac hypertrophy models in neonatal rat ventricular myocytes and human embryonic stem cell-derived cardiomyocytes. Our results demonstrated a significant reduction in KLF2 expression during the progression of cardiac hypertrophy. In vitro , Klf2 deficiency exacerbates cardiac hypertrophy and enhances hypertrophic reprogramming, while KLF2 overexpression attenuates cardiac hypertrophy and reverses hypertrophic transcriptome reprogramming. Mechanistically, combined RNA-seq and cleavage under targets & tagmentation (CUT&Tag) analysis revealed that KLF2 exerts its protective effects by directly regulating a set of genes associated with cardiac hypertrophy. In vivo , KLF2 overexpression specifically in cardiomyocytes effectively prevents TAC-induced cardiac hypertrophy in mice. Additionally, we found that simvastatin elevates KLF2 expression in cardiomyocytes, which subsequently alleviates cardiomyocyte hypertrophy. This study provides the first evidence that transcription factor KLF2 serves as a negative regulator of cardiac hypertrophy. Our findings highlight the therapeutic potential of enhancing KLF2 expression, particularly through simvastatin administration, as a promising strategy in the treatment of cardiac hypertrophy. The present study demonstrates that the transcription factor KLF2 negatively regulates cardiac hypertrophy. Under phenylephrine treatment or pressure overload conditions, the expression of KLF2 was reduced, and KLF2 deficiency exacerbates cardiac hypertrophy and enhances hypertrophic reprogramming. In contrast, AAV-CTNT-delivery or simvastatin treatment significantly increases the expression of KLF2, leading to the downregulation of hypertrophic genes, and ultimately preventing the progression of cardiac hypertrophy. [Display omitted] • This study for the first time elucidates the role of Krüppel-like factor 2 (KLF2) in cardiomyocytes, and reveals its function as a negative regulator of cardiac hypertrophy. • KLF2 in cardiomyocytes mediates the inhibitory effects of simvastatin against cardiomyocyte hypertrophy. • Targeting KLF2 may represent a novel therapeutic approach against cardiac hypertrophy. Given the inhibitory effect of KLF2 on cardiac hypertrophy, it is imperative to explore the clinical benefits of KLF2 activators including simvastatin for patients suffering from this condition. [ABSTRACT FROM AUTHOR]

Hemoglobin subunits, which form the well-characterized, tetrameric, oxygen-carrying protein, have recently been described to be expressed in various non-canonical cell types. However, the exact function of hemoglobin subunits within these cells remains to be fully elucidated. Herein, we report for the first time, the expression of hemoglobin alpha-a1 (Hba-a1) in T-lymphocytes and describe its role as a mitochondrial-associated antioxidant. Within naïve T-lymphocytes, Hba-a1 mRNA and HBA protein are present and highly induced by redox perturbations, particularly those arising from the mitochondria. Additionally, preliminary data using a T-lymphocyte specific Hba-a1 knock-out mouse model indicated that the loss of Hba-a1 led to an exacerbated production of mitochondrial reactive oxygen species and inflammatory cytokines after a stress challenge, further supporting the role of HBA acting to buffer the mitochondrial redox environment. Interestingly, we observed Hba-a1 expression to be significantly upregulated or downregulated depending on T-lymphocyte polarization and metabolic state, which appeared to be controlled by both transcriptional regulation and chromatin remodeling. Altogether, these data suggest Hba-a1 may function as a crucial mitochondrial-associated antioxidant and appears to possess critical and complex functions related to T-lymphocyte activation and differentiation. [Display omitted] • Hemoglobin alpha is expressed and is functional in mouse and human T-lymphocytes. • Activation and polarization of T-lymphocytes dramatically alters hemoglobin expression. • T-lymphocyte hemoglobin impacts mitochondrial function and reactive oxygen species (ROS). • Hemoglobin alpha is redox-responsive in naïve T-lymphocytes, but silenced in activated cells. • Loss of hemoglobin alpha in T-lymphocytes causes potentiated mitochondrial ROS and inflammation. [ABSTRACT FROM AUTHOR]

Despite the ongoing epidemic of youth vaping, the long-term health consequences of electronic cigarette use are largely unknown. We report the effects of vaping versus smoking on the oral cell methylome of healthy young vapers and smokers relative to nonusers. Whereas vapers and smokers differ in the number of differentially methylated regions (DMRs) (831 vs. 2,863), they share striking similarities in the distribution and patterns of DNA methylation, chromatin states, transcription factor binding motifs, and pathways. There is substantial overlap in DMR-associated genes between vapers and smokers, with the shared subset of genes enriched for transcriptional regulation, signaling, tobacco use disorders, and cancer-related pathways. Of significance is the identification of a common hypermethylated DMR at the promoter of HIC1 (hypermethylated in cancer 1), a tumor suppressor gene frequently silenced in smoking-related cancers. Our data support a potential link between epigenomic dysregulation in youth vapers and disease risk. These novel findings have significant implications for public health and tobacco product regulation. [ABSTRACT FROM AUTHOR]

Anillin (ANLN), a mitotic protein that regulates contractile ring assembly, has been reported as an oncoprotein. However, the function of ANLN in cancer cells, especially in the nucleus, has not been fully understood. Here, we report a role of nuclear ANLN in gene transcriptional regulation. We find that nuclear ANLN directly interacts with the RNA polymerase II (Pol II) large subunit to form transcriptional condensates. ANLN enhances initiated Pol II clustering and promotes Pol II CTD phase separation. Short-term depletion of ANLN alters the chromatin binding and enhancer-mediated transcriptional activity of Pol II. The target genes of ANLN-Pol II axis are involved in oxidoreductase activity, Wnt signaling and cell differentiation. THZ1, a super-enhancer inhibitor, specifically inhibits ANLN-Pol II clustering, target gene expression and esophageal squamous cell carcinoma (ESCC) cell proliferation. Our results reveal the function of nuclear ANLN in transcriptional regulation, providing a theoretical basis for ESCC treatment. The oncoprotein ANLN regulates contractile ring assembly during mitosis, has been reported as an oncoprotein. Here, the authors report a role of nuclear ANLN in gene transcriptional regulation through interaction with RNA Pol II and promoting its clustering and phase separation. [ABSTRACT FROM AUTHOR]

Background: RNA polymerase-binding protein A (RbpA) is an actinomycetes-specific protein crucial for the growth and survival of the pathogen Mycobacterium tuberculosis. Its role is essential and influences the transcription and antibiotic responses. However, the regulatory mechanisms underlying RbpA-mediated transcription remain unknown. In this study, we employed various computational techniques to investigate the role of RbpA in the formation and dynamics of the RNA polymerase complex. Results: Our analysis reveals significant structural rearrangements in RNA polymerase happen upon interaction with RbpA. Hotspot residues, crucial amino acids in the RbpA-mediated transcriptional regulation, were identified through our examination. The study elucidates the dynamic behavior within the complex, providing insights into the flexibility and functional dynamics of the RbpA-RNA polymerase interaction. Notably, potential allosteric mechanisms, involving the interface of subunits α1 and α2 were uncovered, shedding light on how RbpA modulates transcriptional activity. Conclusions: Finally, potential ligands meant for the α1–α2 binding site were identified through virtual screening. The outcomes of our computational study serve as a foundation for experimental investigations into inhibitors targeting the RbpA-regulated dynamics in RNA polymerase. Overall, this research contributes valuable information for understanding the intricate regulatory networks of RbpA in the context of transcription and suggests potential avenues for the development of RbpA-targeted therapeutics. [ABSTRACT FROM AUTHOR]

In our research, we performed temporal transcriptomic profiling of host cells infected with Equid alphaherpesvirus 1 (EHV-1) by utilizing direct cDNA sequencing based on nanopore MinION technology. The sequencing reads were harnessed for transcript quantification at various time points. Viral infection-induced differential gene expression was identified through the edgeR package. The identified genes were segmented into six groups based on their kinetic characteristics. The initial three clusters encompass immediate-early response genes, typically transcription factors and elements of antiviral signaling pathways. These genes were either upregulated (cluster 1) or downregulated (clusters 2 and 3) during the early infection phase. The remaining three clusters include late response genes. In these categories, it is challenging to determine whether changes in gene expression are directly connected to the viral infection or merely side effects of the infection. A study of gene associations using the STRINGDB software revealed several gene networks that might be directly impacted by the virus. We also explored whether gene co-expression could be a result of their collective regulation by upstream transcription factors using the Gene Regulatory Network database. Finally, our differential transcript usage (DTU) analysis identified a number of genes that exhibited altered proportions of transcript isoforms in comparison to non-infected cells. Thus, our analysis revealed that EHV-1 infection not only alters host gene expression but also leads to differential use of transcript isoforms, particularly splice variants. [ABSTRACT FROM AUTHOR]

Introduction: The regulation of Cd4 expression during T-cell development and immune responses is essential for proper lineage commitment and function in the periphery. However, the mechanisms of genetic and epigenetic regulation are complex, and their interplay not entirely understood. Previously, we demonstrated the need for CD4 upregulation during positive selection to ensure faithful commitment of MHC-II-restricted T cells to the CD4 lineage. In this study, we investigate whether a conserved region, here called NCE, that is proximal to the Cd4 silencer and contains E4m has the required developmental-stage-specific canonical enhancer function and TCR responsiveness to mediate the CD4 upregulation required to prevent lineage errors. Methods: To investigate the role of NCE, transient transfection of reporter plasmids was performed in thymoma cell lines arrested at the double-positive (DP, CD4+CD8+) and intermediate (INT, CD4+CD8lo) stages of development. CRISPR/Cas9-mediated deletion of the coreNCE/E4m region was carried out in these cell lines to assess its impact on CD4 surface expression, re-expression rates, and TCR signaling responsiveness. To avoid developmental alterations from direct manipulation of the endogenous Cd4 locus in vivo , BAC-transgenic reporter mice were generated with the locus modified to express EGFP in the presence or absence of NCE. EGFP mRNA levels were measured via RT-qPCR, and EGFP fluorescence was analyzed in post-selection thymocytes. Results: Our in vitro experiments demonstrate that NCE by itself can function as an enhancer at the INT, but not the DP stage of development. Furthermore, CRISPR/Cas9-mediated deletion of coreNCE/E4m resulted in reduced CD4 surface levels, slower re-expression rates, and reduced TCR signaling responsiveness in INT cells, but not in DP cells. In vivo , NCE-sufficient transgenic mice exhibited upregulation of Cd4 reporter EGFP mRNA levels at the INT stage and a corresponding upregulation of EGFP fluorescence, whereas NCE-deficient mice showed a significant loss of Cd4 reporter EGFP mRNA and no detectable EGFP production in any post-selection thymocytes. Discussion: This study demonstrates that the canonical enhancer function of coreNCE/E4m is essential for CD4 upregulation following positive selection. The NCE region, with its developmental-stage-specific activity and its known epigenetic regulatory capabilities, ensures faithful lineage commitment to the CD4 lineage. [ABSTRACT FROM AUTHOR]

Genotype-informed anticancer therapies such as BRAF inhibitors can show remarkable clinical efficacy in BRAF-mutant melanoma; however, drug resistance poses a major hurdle to successful cancer treatment. Many resistance events to targeted therapies have been identified, suggesting a complex path to improve therapeutics. Here, we showed the utility of a piggyBac transposon activation mutagenesis screen for the efficient identification of genes that are resistant to BRAF inhibition in melanoma. Although several forward genetic screens performed in the same context have identified a broad range of resistance genes that poorly overlap, an integrative analysis revealed a much smaller functional diversity of resistance mechanisms, including reactivation of the MAPK pathway, PI3K-AKT pathway, and Hippo pathway, suggesting that a relatively small number of therapeutic strategies might overcome resistance manifested by a large gene set. Moreover, we illustrated the pivotal role of the Hippo pathway effector TAZ (encoded by the WWTR1 gene) in mediating BRAF inhibition resistance through transcriptional regulation of receptor tyrosine kinases and through interactions with the E3 ubiquitin ligase NEDD4L. [ABSTRACT FROM AUTHOR]

The organization of the human genome in space and time is critical for transcriptional regulation and cell fate determination. However, robust methods for tracking genome organization or genomic interactions over time in living cells are lacking. Here, we developed a multicolor DNA labeling system, ParSite, to simultaneously track triple genomic loci in the U2OS cells. The tricolor ParSite system is derived from the T. thermophilus ParB/ParSc (TtParB/ParSc) system by rational design. We mutated the interface between TtParB and ParSc and generated a new pair of TtParBm and ParSm for genomic DNA labeling. The insertions of 16 base-pair palindromic ParSc and ParSm into genomic loci allow dual-color DNA imaging in living cells. A pair of genomic loci labeled by ParSite could be colocalized with p53-binding protein 1 (53BP1) in response to CRISPR/Cas9-mediated double-strand breaks (DSBs). The ParSite permits tracking promoter and terminator dynamics of the APP gene, which spans 290 kilobases in length. Intriguingly, the hybrid ParS (ParSh) of half-ParSc and half-ParSm enables for the visualization of a third locus independent of ParSc or ParSm. We simultaneously labeled 3 loci with a genomic distance of 36, 89, and 352 kilobases downstream the C3 repeat locus, respectively. In sum, the ParSite is a robust DNA labeling system for tracking multiple genomic loci in space and time in living cells. Live cell imaging tools are used to study chromatin dynamics over time, but a simple and versatile multicolor DNA imaging method is still needed. This study develops ParSite, based on the T. thermophilus ParB/ParS system, that allows for tri-color genomic DNA imaging in living cells. [ABSTRACT FROM AUTHOR]

Chromatin structure and DNA accessibility are partly modulated by the incorporation of histone variants. H2A.Z, encoded by the non-essential HTZ1 gene in S. cerevisiae, is an evolutionarily conserved H2A histone variant that is predominantly incorporated at transcription start sites by the SWR1-complex (SWR1-C). While H2A.Z has often been implicated in transcription regulation, htz1Δ mutants exhibit minimal changes in gene expression compared to wild-type. However, given that growth defects of htz1Δ mutants are alleviated by simultaneous deletion of SWR1-C subunits, previous work examining the role of H2A.Z in gene expression regulation may be confounded by deleterious activity caused by SWR1-C when missing its H2A.Z substrate (apo-SWR1-C). Furthermore, as H2A.Z mutants only display significant growth defects in genotoxic stress conditions, a more substantive role for H2A.Z in gene expression may only be uncovered after exposure to cellular stress. To explore this possibility, we generated mRNA transcript profiles for wild-type, htz1Δ, swr1Δ, and htz1Δswr1Δ mutants before and after exposure to hydroxyurea (HU), which induces DNA replication stress. Our data showed that H2A.Z played a more prominent role in gene activation than repression during HU exposure, and its incorporation was important for proper upregulation of several HU-induced genes. We also observed that apo-SWR1-C contributed to gene expression defects in the htz1Δ mutant, particularly for genes involved in phosphate homeostasis regulation. Furthermore, mapping H2A.Z incorporation before and after treatment with HU revealed that decreases in H2A.Z enrichment at transcription start sites was correlated with, but generally not required for, the upregulation of genes during HU exposure. Together this study characterized the regulatory effects of H2A.Z incorporation during the transcriptional response to HU. Author summary: Chromatin structure is involved in all aspects of genome function and can be remodelled through a variety of different mechanisms. One foundational aspect of chromatin biology is the incorporation of the histone variant H2A.Z by the SWR1-C chromatin remodelling complex, which results in the formation of structurally distinct regions with diverse biological functions. Despite a general understanding of the basic biology of H2A.Z, many key aspects related to its relationship with SWR1-C, as well as its involvement in gene expression regulation, have remained long-standing enigmas within the field. Here, we take advantage of budding yeast as a model system to examine how preventing H2A.Z incorporation affects the transcriptional response to hydroxyurea (HU) exposure, a genotoxic agent which induces DNA replication stress. In general, we found that H2A.Z played a more prominent role in gene activation than repression during HU exposure, and that its incorporation was essential for many HU-induced genes to achieve wild-type levels of expression. Our results indicate that for future studies to effectively examine the role of H2A.Z in transcription regulation, it is important to account for both the confounding effects of SWR1-C and to examine gene expression before and after gene induction. [ABSTRACT FROM AUTHOR]

Among the various sources of selenium supplementations, the Se-methylselenocysteine (SeMC) is a natural organic selenium compound that has been demonstrated to have multiple advantages in terms of metabolism efficiency and biosafety in animals. Nevertheless, the genome-wide impact of SeMC on gene transcription remains to be elucidated. In this study, we employed an LPS-stimulated chicken HD11 macrophage-like cell model to identify the principal transcription factors involved in transcriptome regulation responsible for SeMC treatment. RNA-seq identified 3,263 transcripts that exhibited a statistically significant differential expression between the SeMC-treated group and the control group and 1,344 transcripts that exhibited a statistically significant differential expression between the LPS + SeMC- and LPS-treated groups (FDR < 0.05, FDR > 1.5). The bioinformatic analysis identified six transcription factors (NFKB2, RFX2, E2F5, ETV5, BACH1, and E2F7) as potential candidate genes for transcriptome regulation in SeMC-treated HD11 cells. Subsequent experimental verification demonstrated that SeMC suppressed the inflammatory response in an LPS-stimulated chicken HD11 cell model via the TXN2—NF-κB pathway. The administration SeMC was observed to reduce the production of ROS as well as the transcription and translation of inflammatory cytokines in both cell culture and in vivo animal studies. One candidate pathway by which SeMC exerts its effects is through the targeting of the transcription factor, NFKB2, by selenoprotein TXN2. This study identified key transcription factors and revealed one of the potential mechanisms through which SeMC exerts its anti-inflammatory effects from the perspective of transcriptional regulation. [ABSTRACT FROM AUTHOR]

Mycobacterium tuberculosis (Mtb) is the pathogenic agent of tuberculosis (TB). Intracellular survival plays a central role in the pathogenesis of Mtb in a manner that is dependent on an array of transcriptional regulators for Mtb. However, the functionality of JTY_0672, a member of the TetR family of transcriptional regulators, remains unknown. In this study, EMSA, BIL, ChlP-PCR and animal models were used to investigate the regulation function of this protein. We found that the transcriptional regulator JTY_0672 is a broad-spectrum transcriptional regulatory protein and can directly regulate JTY_3148 , both in vitro and in vivo. Cofactors containing V B 1, V B 3, V B 6, V C , His, Cys, Asp, Glu, Fe3+, Pb2+, Cu2+, and Li+ were found to inhibit binding between JTY_0672 and the promoter of JTY_3148. JTY_0672 enhanced TAG production and increased Isoniazid (INH) resistance. Besides, this protein either promoted recalcitrance to the host immune response and induced pathological injury and inflammation. In summary, this research identified new targets and cofactors of JTY_0672 and deciphered the physiological functionality of JTY_0672. Our findings will provide an important theoretical basis for understanding the Mtb transcriptional regulatory mechanism. [ABSTRACT FROM AUTHOR]

Introduction: A continuing challenge for malaria control is the ability of Plasmodium falciparum to develop resistance to antimalarial drugs. Members within the Plasmodium transcription factor family AP2 regulate the growth and development of the parasite, and are also thought to be involved in unclear aspects of drug resistance. Here we screened for single nucleotide polymorphisms (SNPs) within the AP2 family and identified 6 non-synonymous mutations within AP2-06B (PF3D7_0613800), with allele frequencies greater than 0.05. One mutation, K3124R, was located in a PfAP2-06B AP2 domain. Methods: To investigate transcriptional regulation by PfAP2-06B, ChIP-seq assays were performed on 3D7/PfAP2-06B-GFP schizonts using antibodies against GFP. The DNA sequences of the artemisinin-resistant CWX and the quinoline-resistant strains PfDd2 and Pf7G8 were analyzed for the genetic diversity of AP2-06B, compared with the Pf3D7 strain as a reference sequence. To determine whether AP2-06B can alter the expression of pfk13 and pfcrt , as well as cause artemisinin and quinoline resistance in Plasmodium , we generated both a K3124R mutation and conditional knockdown of AP2-06B in Pf3D7 using CRISPR/Cas9-mediated genome editing. Results: ChIP-Seq analysis showed that AP2-06B can bind to the loci of the Plasmodium genes pfk13 and pfcrt. The AP2-06B K3124R mutation was also found in the artemisinin-resistant parasite strain CWX and the chloroquine-resistant strains Dd2 and 7G8. Contrary to expectation, Pf3D7 Plasmodium lines modified by either K3124R mutation of AP2-06B or conditional knockdown of AP2-06B did not have altered sensitivity to artemisinin or quinolines by modulating pfk13 or pfcrt expression. Discussion: AP2-06B was predicted to be associated with artemisinin and quinoline resistance, but no change in resistance was observed after mutation or conditional knockdown. Given the multigenic nature of resistance, it might be difficult to recreate a resistance phenotype. In conclusion, whether AP2-06B regulates the development of artemisinin or quinoline resistance remains to be studied. [ABSTRACT FROM AUTHOR]

Flesh firmness is a core quality trait in apple breeding because of its correlation with ripening and storage. Quantitative trait loci (QTLs) were analyzed through bulked segregant analysis sequence (BSA-seq) and comparative transcriptome analysis (RNA-seq) to explore the genetic basis of firmness formation. In this study, phenotypic data were collected at harvest from 251 F1 hybrids derived from 'Ruiyang' and 'Scilate', the phenotype values of flesh firmness at harvest were extensively segregated for two consecutive years. A total of 11 candidate intervals were identified on chromosomes 03, 05, 06, 07, 13, and 16 via BSA-seq analysis. We characterized a major QTL on chromosome 16 and selected a candidate gene encoding expansin MdEXP-A1 by combining RNA-seq analysis. Furthermore, the genotype of Del-1166 (homozygous deletion) in the MdEXP-A1 promoter was closely associated with the super-hard phenotype of F1 hybrids, which could be used as a functional marker for marker-assisted selection (MAS) in apple. Functional identification revealed that MdEXP-A1 positively expedited fruit softening in both apple fruits and tomatoes that overexpressed MdEXP-A1. Moreover, the promoter sequence of TE-1166 was experimentally validated containing two binding motifs of MdNAC1, and the absence of the MdEXP-A1 promoter fragment reduced its transcription activity. MdNAC1 also promotes the expression of MdEXP-A1, indicating its potential modulatory role in quality breeding. These findings provide novel insight into the genetic control of flesh firmness by MdEXP-A1. [ABSTRACT FROM AUTHOR]

Background: Hyaluronic acid (HA) is extensively employed in various fields such as medicine, cosmetics, food, etc. The molecular weight (MW) of HA is crucial for its biological functions. Streptococcus zooepidemicus, a prominent HA industrial producer, naturally synthetizes HA with high MW. Currently, few effective approaches exist for the direct and precise regulation of HA MW through a one-step fermentation process, and S. zooepidemicus lacks metabolic regulatory elements with varying intensities. The ratio of HA's precursors, UDP-N-acetylglucosamine (UDP-GlcNAc) and UDP-glucuronic acid (UDP-GlcA), is critical for the extension and release of HA. An imbalance in the precursor proportions for HA synthesis leads to a significant decrease in HA MW, indicating that controlling the precursor ratio may serve as a potential method for regulating HA MW. Results: In this study, the type and concentration of carbon sources were manipulated to disrupt the balance of precursor supply. Based on the results, it was speculated that the transcription level of hasE, which may connect the two HA synthesis precursors, is positively correlated with HA MW. Consequently, an endogenous expression component library for S. zooepidemicus was constructed, comprising 32 constitutive and 4 inducible expression elements. The expression of hasE was subsequently regulated in strain SE0 (S12 ΔhasE) using two constitutive promoters of differing strengths. The recombinant strain SE1, in which hasE was controlled by the stronger promoter PR31, produced HA with a MW of 1.96 MDa. In contrast, SE2, utilizing the weaker promoter PR22, synthesized shorter HA with a MW of 1.63 MDa, thereby verifying the hypothesis. Finally, to precisely regulate HA MW according to specific demands, an efficient sucrose-induced expression system was screened and employed to control the transcription level of hasE, obtaining recombinant strain SE3. When induced with sucrose concentrations of 3, 5–10 g/L, the HA MW of SE3 reached 0.78 to 1.77 MDa, respectively. Conclusions: Studies on regulating the balance of the HA precursor substances indicate that an oversupply of either UDP-GlcNAc or UDP-GlcUA can reduce HA MW. The hasE gene serves as a crucial regulator for maintaining this balance. Precise regulation of hasE transcription was achieved through an efficient inducible expression system, enabling the customized production of HA with specific MW. The HA MW of strain SE3 can be accurately manipulated by adjusting sucrose concentration, establishing a novel strategy for customized HA fermentation. [ABSTRACT FROM AUTHOR]

Lactylation, a post-translational modification, has been linked to gene transcription regulation through epigenetic modulation in various pathophysiological processes. The lactylation regulatory proteins, known as writers, erasers, and readers, govern their dynamics by adding, removing, and recognizing lactyl groups on proteins. Macrophages, as cells of the immune system, maintain homeostasis, responding dynamically to diverse internal and external stimuli. Emerging researches unveil that lactylation, through inducing macrophage activation and polarization, affects their functionality in pathological conditions such as inflammation, tumor microenvironment, and fibrosis. Evidence progressively indicates that lactate-driven alterations in lactylation levels within macrophages can influence the pathogenesis of numerous diseases. This review aims to systematically summarize the research progress of lactylation in macrophages, explore its functions and mechanisms by which lactylation contributes to the pathology of different disease phenotypes, and propose future research directions along with potential diagnostic and therapeutic strategies. [ABSTRACT FROM AUTHOR]

Astrocytes produce and export glutathione (GSH), an important thiol antioxidant essential for protecting neural cells from oxidative stress and maintaining optimal brain health. While it has been established that oxidative stress increases GSH production in astrocytes, with Nrf2 acting as a critical transcription factor regulating key components of the GSH synthetic pathway, the role of Nrf2 in controlling constitutive GSH synthetic and release mechanisms remains incompletely investigated. Our data show that naïve primary mouse astrocytes cultured from the cerebral cortices of Nrf2 knockout (Nrf2−/−) pups have significantly less intracellular and extracellular GSH levels when compared to astrocytes cultured from Nrf2 wild-type (Nrf2+/+) pups. Key components of the GSH synthetic pathway, including xCT (the substrate-specific light chain of the substrate-importing transporter, system xc−), glutamate-cysteine ligase [catalytic (GCLc) and modifying (GCLm) subunits], were affected. To wit: qRT-PCR analysis demonstrates that naïve Nrf2−/− astrocytes have significantly lower basal mRNA levels of xCT and both GCL subunits compared to naïve Nrf2+/+ astrocytes. No change in mRNA levels of glutathione synthetase (GS) or the GSH exporting transporter, Mrp1, was found. Western blot analysis reveals reduced protein levels of both subunits of GCL, while (seleno)cystine uptake into Nrf2−/− astrocytes was reduced compared to Nrf2+/+ astrocytes, confirming decreased system xc− activity. These findings suggest that Nrf2 regulates the basal production of GSH in astrocytes through constitutive transcriptional regulation of GCL and xCT. [ABSTRACT FROM AUTHOR]

Silencers, the yin to enhancers' yang, play a pivotal role in fine-tuning gene expression throughout the genome. However, despite their recognized importance, comprehensive identification of these regulatory elements in the genome is still in its early stages. We developed a method called Ss-STARR-seq to directly determine the activity of silencers in the whole genome. In this study, we applied Ss-STARR-seq to human cell lines K562, LNCaP, and 293 T, and identified 134,171, 137,753, and 125,307 silencers on a genome-wide scale, respectively, these silencers function in various cells in a cell-specific manner. Silencers exhibited a substantial enrichment of transcriptional-inhibitory motifs, including REST, and demonstrated overlap with the binding sites of repressor transcription factors within the endogenous environment. Interestingly, H3K27me3 did not reflect silencer activity but facilitated the silencer's inhibitory role on gene expression. Additionally, the silencer did not have any significant histone markers at the genome-wide level. Our findings unveil that aspect-silencers not only transition into enhancers throughout diverse cell lines but also achieve functional conversion with insulators. Regarding to biological effects, knockout experiments underscored the functional redundancy and specificity of silencers in regulating gene expression and cell proliferation. In summary, this study pioneers the elucidation of the genome-wide silencer landscape in human cells, delineates their global regulatory features, and identifies specific silencers influencing cancer cell proliferation. Silencers play a critical role in gene transcription regulation. Here, the authors developed the Ss-STARR-seq technique to identify tens of thousands of silencers in human cells. These silencers possess unique epigenetic features and are capable of influencing cellular phenotypes. [ABSTRACT FROM AUTHOR]

Heat stress adversely impacts plant growth, development, and grain yield. Heat shock factors (Hsf), especially the HsfA2 subclass, play a pivotal role in the transcriptional regulation of genes in response to heat stress. In this study, the coding sequence of maize ZmHsf17 was cloned. ZmHsf17 contained conserved domains including a DNA binding domain, oligomerization domain, and transcriptional activation domain. The protein was nuclear localized and had transcription activation activity. Yeast two-hybrid and split luciferase complementation assays confirmed the interaction of ZmHsf17 with members of the maize HsfA2 subclass. Overexpression of ZmHsf17 in maize significantly increased chlorophyll content and net photosynthetic rate, and enhanced the stability of cellular membranes. Through integrative analysis of ChIP-seq and RNA-seq datasets, ZmPAH1 , encoding phosphatidic acid phosphohydrolase of lipid metabolic pathways, was identified as a target gene of ZmHsf17. The promoter fragment of ZmPAH1 was bound by ZmHsf17 in protein–DNA interaction experiments in vivo and in vitro. Lipidomic data also indicated that the overexpression of ZmHsf17 increased levels of some critical membrane lipid components of maize leaves under heat stress. This research provides new insights into the role of the ZmHsf17–ZmPAH1 module in regulating thermotolerance in maize. [ABSTRACT FROM AUTHOR]

Angiosperms are the most dominant land plant flora and have colonized most of the terrestrial habitats, thriving in different environmental conditions, among which light and temperature play a crucial role. In the eudicot Arabidopsis thaliana , light and temperature are integrated into a phytochrome B (phyB)-dependent signalling network that regulates development. However, whether this signal integration controls the development in other angiosperm lineages and whether phyB is a conserved hub of this integratory network in angiosperms is unclear. We used a combination of phylogenetic, phenotypic, and transcriptomic analyses to understand the phyB-dependent light and temperature integratory network in the monocot Oryza sativa and infer its conservation in angiosperms. Here, we showed that light and temperature co-regulate rice growth through a phyB-dependent regulatory network that shares conserved features between O. sativa and A. thaliana. Despite the conservation of the components of this regulatory network, the transcriptional regulation between the components has changed qualitatively since monocots and eudicots diverged (~192–145 million years ago). The evolutionary flexibility of this integratory network might underlie the successful adaptation of plants to diverse ecological niches. Furthermore, our findings provide promising candidate genes whose activity and expression can be fine-tuned to improve plant growth and productivity in a warming planet. [ABSTRACT FROM AUTHOR]

Banana is sensitive to cold stress and often suffers from chilling injury with browning peel and failure to normal ripening. We have previously reported that banana chilling injury is accompanied by a reduction of miR528 accumulation, alleviating the degradation of its target gene MaPPO and raising ROS levels that cause peel browning. Here, we further revealed that the miR528-MaPPO cold-responsive module was regulated by miR156-targeted SPL transcription factors, and the miR156c-MaSPL4 module was also responsive to cold stress in banana. Transient overexpression of miR156c resulted in a more severe chilling phenotype by decreasing the expression of MaSPL4 and miR528. Conversely, the browning was alleviated in STTM-miR156c silencing and OE-MaSPL4 samples. Furthermore, DNA affinity purification sequencing and MaSPL4-overexpressing transcriptome jointly revealed that MaSPL4 may mediate the transcription of genes related to lipid metabolism and antioxidation, in addition to the miR528-MaPPO module, demonstrating MaSPL4 as a master regulator in the fruit cold response network. In summary, our results suggest that the miR156c-MaSPL4 module can mediate the chilling response in banana by regulating the miR528-MaPPO module and multiple other pathways, which provides evidence for the crosstalk between TFs and miRNAs that can be used for the molecular breeding of fruit cold tolerance. [ABSTRACT FROM AUTHOR]

Ischemic stroke constitutes a multifaceted neurological affliction that spans various cellular types. Lack of dynamic chromatin accessibility data after stroke is one of the obstacles to understanding this process. To gain insights into the variations in transcriptional regulation among various cell types subsequent to a stroke, we employed single-nucleus ATAC-seq to curate a chromatin accessibility compendium from the cerebral cortex of mice subjected to middle cerebral artery occlusion/reperfusion (MCAO/R). Tissue samples were collected at various time points including 0, 6, 12, 24 hours, and 7, 14 days post-reperfusion, in addition to Sham control group. We obtained 99,271 high-quality nuclei across nine cell types, thereby establishing the single-nucleus chromatin accessibility atlas. This atlas provides data for interpreting the regulatory mechanisms that pervade the continuum of ischemic stroke. The data presented herein constitutes a valuable resource for the comprehension of regulatory interplays within the pathology-afflicted cerebrum. [ABSTRACT FROM AUTHOR]

Chromatin remodellers utilise energy generated from ATP hydrolysis to remodel nucleosomes and modulate histones, which are crucial for eukaryotic gene expression and chromatin architecture. The SWI/SNF (switching defective/sucrose non-fermenting) class of ATP-dependent chromatin modifiers in eukaryotes includes two complexes, SWI/SNF and RSC (remodeling the structure of chromatin). In the past 10 years, SWI/SNF and RSC chromatin remodellers have been a focus of research in various organisms, including animals, plants and fungi. In fungi, these two complexes have multiple functions, including roles in regulating hyphal differentiation, sporulation, stress responses, and pathogenicity. In addition to describing conserved structural properties and mechanisms of action, we highlight evidence for sequence and functional divergence in fungal evolution. This review provides a basis for further comparative analyses of the roles and regulatory mechanisms of the SWI/SNF and RSC complexes in taxonomically diverse fungi, laying a good foundation for potential applications in controlling pathogenic fungi. [ABSTRACT FROM AUTHOR]

Post-transcriptional mechanisms, such as alternative splicing and polyadenylation, are recognized as critical regulatory processes that increase transcriptomic and proteomic diversity. The advent of next-generation sequencing and whole-genome analyses has revealed that numerous transcription and epigenetic regulators, including transcription factors and histone-modifying enzymes, undergo alternative splicing, most notably in the nervous system. Given the complexity of regulatory processes in the brain, it is conceivable that many of these splice variants control different aspects of neuronal development. Mutations or dysregulation of splicing and transcription regulatory proteins are frequently linked to various neurodevelopmental disorders, highlighting the importance of understanding the role of neuron-specific alternative splicing in maintaining proper transcriptional regulation in the brain. This review consolidates current insights into the role of alternative splicing in influencing transcriptional and chromatin regulatory programs in neuronal development. [ABSTRACT FROM AUTHOR]

The selection of plant genotypes characterized by wellness and stable growth under drought-stress conditions amid ongoing climate change is an important challenge in forest tree breeding. The introduction of molecular markers will enable efficient selection of breeding materials that are resistant to drought stress in forest trees as well as in crop species. Japanese cedar, Cryptomeria japonica (Thunb. ex L.f.) D. Don, the most dominant forest species in Japan, grows well on mesic sites and is characterized by intraspecific variation in its drought-stress response. Here, we analyzed the physiological characteristics and gene expression profiles of multiple C. japonica genotypes under both control and drought-stress conditions to identify drought-responsive genes and develop gene expression markers that could assess the physiological status of cuttings based on their gene expression responses to dehydration. The two representative genes that showed a large expressional change in the later period after water withholding were both homologs of COR47 , a gene in the dehydrin protein family, and of ERF016 , a member of the dehydration-responsive element-binding transcription factor family in Arabidopsis. We developed both intermediate- and small-scale sets of gene-expression analysis platforms that allowed us to correlate gene expression with the physiological responses of cuttings to drought. The results highlight the potential to assess the environmental adaptability with gene expression analysis in C. japonica. [ABSTRACT FROM AUTHOR]

Evolutionary events leading to organismal preference for a specific growth temperature, as well as genes whose products are needed for a proper function at that temperature, are poorly understood. Using 64 bacteria from phylum Thermotogota as a model system, we examined how optimal growth temperature changed throughout Thermotogota history. We inferred that Thermotogota 's last common ancestor was a thermophile and that some Thermotogota evolved the mesophilic and hyperthermophilic lifestyles secondarily. By modeling gain and loss of genes throughout Thermotogota history and by reconstructing their phylogenies, we demonstrated that adaptations to lower and higher growth temperature involve both the acquisition of necessary genes and loss of unnecessary genes. Via a pangenome-wide association study, we correlated presence/absence of 68 genes with specific optimal growth temperature intervals. While some of these genes are poorly characterized, most are involved in metabolism of amino acids, nucleotides, carbohydrates, and lipids, as well as in signal transduction and regulation of transcription. Most of the 68 genes have a history of horizontal gene transfer with other bacteria and archaea that often grow at similar temperatures, suggesting that parallel acquisitions of genes likely promote independent adaptations of different Thermotogota species to specific growth temperatures. [ABSTRACT FROM AUTHOR]

Altered regulatory interactions during development likely underlie a large fraction of phenotypic diversity within and between species, yet identifying specific evolutionary changes remains challenging. Analysis of single-cell developmental transcriptomes from multiple species provides a powerful framework for unbiased identification of evolutionary changes in developmental mechanisms. Here, we leverage a "natural experiment" in developmental evolution in sea urchins, where a major life history switch recently evolved in the lineage leading to Heliocidaris erythrogramma , precipitating extensive changes in early development. Comparative analyses of single-cell transcriptome analysis (scRNA-seq) developmental time courses from H. erythrogramma and Lytechinus variegatus (representing the derived and ancestral states, respectively) reveal numerous evolutionary changes in embryonic patterning. The earliest cell fate specification events and the primary signaling center are co-localized in the ancestral developmental gene regulatory network; remarkably, in H. erythrogramma , they are spatially and temporally separate. Fate specification and differentiation are delayed in most embryonic cell lineages, although in some cases, these processes are conserved or even accelerated. Comparative analysis of regulator-target gene co-expression is consistent with many specific interactions being preserved but delayed in H. erythrogramma , while some otherwise widely conserved interactions have likely been lost. Finally, specific patterning events are directly correlated with evolutionary changes in larval morphology, suggesting that they are directly tied to the life history shift. Together, these findings demonstrate that comparative scRNA-seq developmental time courses can reveal a diverse set of evolutionary changes in embryonic patterning and provide an efficient way to identify likely candidate regulatory interactions for subsequent experimental validation. [ABSTRACT FROM AUTHOR]

Gastric cancer (GC) is the most common malignant tumor of the digestive tract. However, the molecular pathogenesis is not well understood. Through bioinformatic analysis and analyzing clinical tissue samples, we found that E2F1 and E2F7 as well as their potential downstream target MYBL2 were all upregulated in GC tissues and that their expressions correlated with patient prognosis. While knockdown of E2F1 or MYBL2 inhibited cell proliferation and promoted apoptosis, knockdown of E2F7 promoted cell proliferation but had no effects on apoptosis. Chromatin immunoprecipitation and dual luciferase reporter assays demonstrated that MYBL2 was transcriptionally activated and repressed by E2F1 and E2F7, respectively. Importantly, in vitro and ex vivo experiments demonstrated that the effects of E2F1 and E2F7 on GC cell proliferation were significantly attenuated by reversely modulating MYBL2 expression, indicating that MYBL2 is a direct and functionally relevant target of E2F1 and E2F7 in GC cells. Furthermore, the effects of E2F1 and E2F7 on GC cell proliferation through transcriptional regulation of MYBL2 can be mediated by the PI3K/AKT signaling pathway. Interestingly, we found differential nucleocytoplasmic distribution of E2F7 in GC cells with functional relevance. Taken together, our data suggest that targeted therapies of GC may be achieved from three different angles, E2F1, E2F7, and MYBL2 themselves, E2F1/E2F7 expression balance, and E2F7 nuclear localization. [ABSTRACT FROM AUTHOR]

Transcription factors (TFs) are the main regulators of eukaryotic gene expression. The cooperative binding of at least two TFs to genomic DNA is a major mechanism of transcription regulation. Massive analysis of the co-occurrence of overrepresented pairs of motifs for different target TFs studied in ChIP-seq experiments can clarify the mechanisms of TF cooperation. We categorized the target TFs from M. musculus ChIP-seq and A. thaliana ChIP-seq/DAP-seq experiments according to the structure of their DNA-binding domains (DBDs) into classes. We studied homotypic pairs of motifs, using the same recognition model for each motif. Asymmetric and symmetric pairs consist of motifs of remote and close recognition scores. We found that asymmetric pairs of motifs predominate for all TF classes. TFs from the murine/plant 'Basic helix–loop–helix (bHLH)', 'Basic leucine zipper (bZIP)', and 'Tryptophan cluster' classes and murine 'p53 domain' and 'Rel homology region' classes showed the highest enrichment of asymmetric homotypic pairs of motifs. Pioneer TFs, despite their DBD types, have a higher significance of asymmetry within homotypic pairs of motifs compared to other TFs. Asymmetry within homotypic CEs is a promising new feature decrypting the mechanisms of gene transcription regulation. [ABSTRACT FROM AUTHOR]

Ovarian cancer remains one of the leading causes of cancer-related deaths in women. There are several processes that are described to have a causal relationship in ovarian cancer development, progression, and metastasis formation, that occur both at the genetic and epigenetic level. One of the mechanisms involved in its pathogenesis and progression is estrogen signaling. Estrogen receptors (ER) α, ERβ, and G-protein coupled estrogen receptor 1 (GPER1), in concert with various coregulators and pioneer transcription factors, mediate the effects of estrogens primarily by the transcriptional regulation of estrogen responsive genes, thereby exerting pleiotropic effects including the regulation of cellular proliferation and apoptosis. The expression and activity of estrogen receptors and their coregulators have been demonstrated to be regulated by epigenetic mechanisms like histone modifications and DNA methylation. Here, we intend to summarize and to provide an update on the current understanding of epigenetic mechanisms regulating estrogen signaling and their role in ovarian cancer. For this purpose, we reviewed publications on this topic listed in the PubMed database. Finally, we assess to which extent drugs acting on the epigenetic level might be suitable for the treatment of ovarian cancer. [ABSTRACT FROM AUTHOR]

Heartwood, serving as the central constituent of the xylem, plays a crucial role in the growth, development, and resilience of trees. The process of heartwood formation constitutes a complex biological phenomenon influenced by various factors. A thorough examination of the mechanisms underpinning heartwood formation not only enhances our understanding of the growth and developmental paradigms regulating trees but also provides essential theoretical support and practical insights for the timber industry, forestry management, and ecological conservation. This paper offers an overview of the foundational processes involved in heartwood formation in plants. Furthermore, it presents a comprehensive review of the latest research advancements in this domain, covering five key aspects: metabolism, hormonal regulation, transcriptional regulation, cell biology, and environmental influences. This review serves as a valuable basis for future research endeavors in related academic fields. [ABSTRACT FROM AUTHOR]

Erythroleukemia, a complex myeloproliferative disorder presenting as acute or chronic, is characterized by aberrant proliferation and differentiation of erythroid cells. Although nootkatone, a sesquiterpene derived from grapefruit peel and Alaska yellow cedar, has shown anticancer activity predominantly in solid tumors, its effects in erythroleukemia remain unexplored. This study aimed to investigate the impact of nootkatone and its derivatives on erythroleukemia. Our results demonstrate that the nootkatone derivative nootkatone-(E)-2-iodobenzoyl hydrazone (N2) significantly inhibited erythroleukemia cell proliferation in a concentration- and time-dependent manner. More importantly, N2 induced megakaryocytic differentiation, as evidenced by significant morphological changes, and upregulation of megakaryocytic markers CD41 and CD61. In vivo, N2 treatment led to a marked increase in platelet counts and megakaryocytic cell counts. Mechanistically, N2 activated a crosstalk between the JAK2/STAT3 and PKCδ/MAPK signaling pathways, enhancing transcriptional regulation of key factors like GATA1 and FOS. Network pharmacology and experimental validation confirmed that N2 targeted JAK2, and knockdown of JAK2 abolished N2-induced megakaryocytic differentiation, underscoring JAK2's critical role in erythroleukemia differentiation. In conclusion, N2 shows great promise as a differentiation therapy for erythroleukemia, offering a novel approach by targeting JAK2-mediated signaling pathways to induce megakaryocytic differentiation. [ABSTRACT FROM AUTHOR]

This literature review examines circadian rhythms, highlighting the crucial role of transcription factors in regulating gene expression, influencing plant and animal behavior, and affecting human disease. It examines the roles of basic transcriptional regulation in circadian rhythms, such as histone modifications, chromatin remodeling, and Pol II pausing control. The review also discusses further progress in the fine regulation of circadian rhythms and the importance of transcriptional regulation in circadian rhythms. This paper underscores the significant link between transcription factors and circadian rhythms, highlighting the latter's contribution to improving human well-being. Almost all organisms, from the simplest bacteria to advanced mammals, have a near 24 h circadian rhythm. Circadian rhythms are highly conserved across different life forms and are regulated by circadian genes as well as by related transcription factors. Transcription factors are fundamental to circadian rhythms, influencing gene expression, behavior in plants and animals, and human diseases. This review examines the foundational research on transcriptional regulation of circadian rhythms, emphasizing histone modifications, chromatin remodeling, and Pol II pausing control. These studies have enhanced our understanding of transcriptional regulation within biological circadian rhythms and the importance of circadian biology in human health. Finally, we summarize the progress and challenges in these three areas of regulation to move the field forward. [ABSTRACT FROM AUTHOR]

Plant–plant (interplant) interactions via volatile organic compounds (VOCs) emitted by plants confer antiherbivore capabilities on the plants receiving these VOCs. Interplant interactions occur with both conspecific and heterospecific neighboring plants, relying on VOCs emitted by herbivore-damaged plants as well as unique or constitutively emitted compounds such as isoprene and fragrant grass VOCs. VOCs are taken up through stomata and diffuse across mesophyll cells in leaves. The mechanisms underlying cellular recognition and uptake of VOCs, likely involving receptors and transporters, are not well understood. Chromatin remodeling and transcriptional regulation are the basis for gene activation for defense responses in VOC-receiving plants. VOC-emitting companion plants and VOC biostimulants may provide sustainable agricultural and horticultural technologies. Volatile organic compounds (VOCs) are essential airborne mediators of interactions between plants. These plant–plant interactions require sophisticated VOC-sensing mechanisms that enable plants to regulate their defenses against pests. However, these interactions are not limited to specific plants or even conspecifics, and can function in very flexible interactions between plants. Sensing and responding to VOCs in plants is finely controlled by their uptake and transport systems as well as by cellular signaling via, for example, chromatin remodeling system-based transcriptional regulation for defense gene activation. Based on the accumulated knowledge about the interactions between plants and their major VOCs, companion plants and biostimulants are being developed for practical applications in agricultural and horticultural pest control, providing a sustainable alternative to harmful chemicals. [ABSTRACT FROM AUTHOR]

Myelodysplastic syndrome (MDS) is a heterogeneous myeloid neoplasm that is hallmarked by the acquisition of genetic events that disrupt normal trilineage hematopoiesis and results in bone marrow dysfunction. Somatic genes involving transcriptional regulation, signal transduction, DNA methylation, and chromatin modification are often implicated in disease pathogenesis. The cohesin complex, composed of SMC1, SMC3, RAD21, and either STAG1 or STAG2, has been identified as a recurrent mutational target with STAG2 mutations accounting for more than half of all cohesin mutations in myeloid malignancies. In the last decade, STAG2 cohesin biology has been of great interest given its role in transcriptional activation, association with poorer prognosis, and lack of mutation-specific therapies. This review discusses the clinical landscape of cohesin mutant myeloid malignancies, particularly STAG2 mutant MDS, including molecular features of STAG2 mutations, clinical implications of cohesin mutant neoplasms, and the current understanding of the pathophysiological function of STAG2 mutations in MDS. [ABSTRACT FROM AUTHOR]

Cannabis sativa L. is one of the oldest domesticated crops. Hemp-type cultivars, which predominantly produce non-intoxicating cannabidiol (CBD), have been selected for their fast growth, seed, and fibre production, while drug-type chemovars were bred for high accumulation of tetrahydrocannabinol (THC). We investigated how the generation of CBD-dominant chemovars by introgression of hemp- into drug-type Cannabis impacted plant performance. The THC-dominant chemovar showed superior sink strength, higher flower biomass, and demand-driven control of nutrient uptake. By contrast, the CBD-dominant chemovar hyperaccumulated phosphate in sink organs leading to reduced carbon and nitrogen assimilation in leaves, which limited flower biomass and cannabinoid yield. RNA-seq analyses determined organ- and chemovar-specific differences in expression of genes associated with nitrate and phosphate homeostasis as well as growth-regulating transcription factors that were correlated with measured traits. Among these were genes positively selected for during Cannabis domestication encoding an inhibitor of the phosphate starvation response, SPX DOMAIN GENE3, nitrate reductase, and two nitrate transporters. Altered nutrient sensing, acquisition, or distribution are likely a consequence of adaption to growth on marginal, low-nutrient-input lands in hemp. Our data provide evidence that such ancestral traits may become detrimental for female flower development and consequently overall CBD yield in protected cropping environments. [ABSTRACT FROM AUTHOR]

Opium poppy is a crop of great commercial value as a source of several opium alkaloids for the pharmaceutical industries including morphine, codeine, thebaine, noscapine, and papaverine. Most enzymes involved in benzylisoquinoline alkaloid (BIA) biosynthesis in opium poppy have been functionally characterized, and opium poppy currently serves as a model system to study BIA metabolism in plants. BIA biosynthesis in opium poppy involves two biosynthetic gene clusters associated respectively with the morphine and noscapine branches. Recent reports have shown that genes in the same cluster are co-expressed, suggesting they might also be co-regulated. However, the transcriptional regulation of opium poppy BIA biosynthesis is not well studied. Opium poppy BIA biosynthesis involves three cell types associated with the phloem system: companion cells, sieve elements, and laticifers. The transcripts and enzymes associated with BIA biosynthesis are distributed across cell types, requiring the translocation of key enzymes and pathway intermediates between cell types. Together, these suggest that the regulation of BIA biosynthesis in opium poppy is multilayered and complex, involving biochemical, genomic, and physiological mechanisms. In this review, we highlight recent advances in genome sequencing and single cell and spatial transcriptomics with a focus on how these efforts can improve our understanding of the genomic and cell-specific regulation of BIA biosynthesis. Such knowledge is vital for opium poppy genetic improvement and metabolic engineering efforts targeting the modulation of alkaloid yield and composition. [ABSTRACT FROM AUTHOR]

Significance: Herbal medicines have a long history of comprehensive cancer treatment through various posttranslational modifications (PTMs). Recently, emerging evidence revealed that dysregulation of reactive oxygen species (ROS) and ROS-regulated signaling pathways influence cancer initiation, growth, and progression in a paradoxical role with either low levels or increasing levels of basal ROS. However, ROS-triggered modifications of target proteins in the face of ROS-mediated signal transduction are not fully understood in the anticancer therapies of herbal medicines. In this review, we briefly introduce the PTM-dependent regulations of herbal medicines, and then focus on the current ideals that targeting ROS-dependent PTMs via antioxidant and redox signaling pathways can provide a promising strategy in herbal-based anticancer effects. Recent Advances: Advanced development in highly sensitive mass spectrometry-based techniques has helped utilize ROS-triggered protein modifications in numerous cancers. Accumulating evidence has been achieved in laboratory to extensively ascertain the biological mechanism of herbal medicines targeting ROS in cancer therapy. Two general mechanisms underlining ROS-induced cell signaling include redox state and oxidative modification of target protein, indicating a new perspective to comprehend the intricate dialogues between herbal medicines and cancer cellular contexts. Critical Issues: Complex components of herbal medicines limit the benefits of herbal-based cancer therapies. In this review, we address that ROS-dependent PTMs add a layer of proteomic complexity to the cancer through altering the protein structure, expression, function, and localization. Elaborating ROS-triggered PTMs implicated in cell signaling, apoptosis, and transcriptional regulation function, and the possible cellular signaling, has provided important information about the contribution of many ROS targeting herbal therapies in anticancer effects. Continued optimization of proteomic strategies for PTM analysis in herbal medicines is also briefly discussed. Future Directions: Rigorous evaluations of herbal medicines and proteomic strategies are necessary to explore the aberrant regulation of ROS-triggered antioxidant and redox signaling contributing to the novel protein targets and herbal-associated pharmacological issues. These efforts will eventually help develop more herbal drugs as modern therapeutic agents. Antioxid. Redox Signal. 42, 150–164. [ABSTRACT FROM AUTHOR]

Unlike most species that use telomerase for telomere maintenance, many dipterans, including Drosophila, rely on three telomere-specific retrotransposons (TRs)--HeT-A, TART, and TAHRE--to form tandem repeats at chromosome ends. Although TR transcription is crucial in their life cycle, its regulation remains poorly understood. This study identifies the Mediator complex, E2F1-Dp, and Scalloped/dTEAD as key regulators of TR transcription. Reducing the activity of the Mediator or Sd/dTEAD increases TR expression and telomere length, while overexpressing E2F1-Dp or depleting Rbf1 stimulates TR transcription. The Mediator and Sd/dTEAD regulate this process through E2F1-Dp. CUT&RUN (Cleavage under targets and release using nuclease) analysis shows direct binding of CDK8, Dp, and Sd/dTEAD to telomeric repeats, with motif enrichment revealing E2F-and TEAD-binding sites. These findings uncover the Mediator complex's role in controlling TR transcription and telomere length through E2F1-Dp and Sd, coupling the transcriptional regulation of the TR life cycle with host cell-cycle machinery to protect chromosome ends in Drosophila. [ABSTRACT FROM AUTHOR]

Rhodococcus equi—a facultative intracellular pathogen of macrophages—causes bronchopneumonia in foals and patients who are immunocompromised. Virulent strains of R. equi possess a virulence‐associated plasmid, which encodes a 15‐ to 17‐kDa surface protein called virulence‐associated protein A (VapA). VapA expression is regulated by temperature and pH. Two transcriptional regulators, VirR and VirS, are involved in the transcriptional regulation of vapA. VirR regulates VapA expression through VirS. However, whether VirR directly regulates virS transcription is unclear. In this study, we examined VirR binding to the promoter region of the icgA operon, which contains virS, using the electrophoretic mobility shift assay and DNase I footprinting. VirR bound DNA fragments containing the virR‐icgA intergenic region. Transcription from the promoter in this region was VirR‐dependent and regulated by temperature and pH. The VirR‐binding site contained the LysR‐type transcriptional regulator‐binding consensus motif, T–N11–A. A point mutation (L98E) in the putative ligand‐binding pocket of VirR constitutively activated the icgA promoter. However, no apparent difference was observed in the electrophoretic mobility shift assay and DNase I footprinting using the icgA promoter when L98E VirR was compared with wild‐type VirR. A bacterial two‐hybrid system identified an interaction between VirR and RpoA. Our data reveal that VirR binds the promoter of the icgA operon and directly activates its transcription. Furthermore, the regulation of VapA expression in response to temperature and pH is mediated by VirR. [ABSTRACT FROM AUTHOR]

Liver fibrosis is the major driver of hepatocellular carcinoma and liver disease-related death. Approved antifibrotic therapies are absent and compounds in development have limited efficacy. Increased TGF-β signaling drives collagen deposition by hepatic stellate cells (HSCs)/myofibroblasts. Here, we aimed to dissect the role of the circadian clock (CC) in controlling TGF-β signaling and liver fibrosis. Using CC-mutant mice, enriched HSCs and myofibroblasts obtained from healthy and fibrotic mice in different CC phases and loss-of-function studies in human hepatocytes and myofibroblasts, we investigated the relationship between CC and TGF-β signaling. We explored hepatocyte-myofibroblast communication through bioinformatic analyses of single-nuclei transcriptomes and performed validation in cell-based models. Using mouse models for MASH (metabolic dysfunction-associated steatohepatitis)-related fibrosis and spheroids from patients with liver disease, we performed proof-of-concept studies to validate pharmacological targetability and clinical translatability. We discovered that the CC oscillator temporally gates TGF-β signaling and this regulation is broken in fibrosis. We demonstrate that HSCs and myofibroblasts contain a functional CC with rhythmic expression of numerous genes, including fibrogenic genes. Perturbation studies in hepatocytes and myofibroblasts revealed a reciprocal relationship between TGF-β activation and CC perturbation, which was confirmed in patient-derived ex vivo and in vivo models. Pharmacological modulation of CC-TGF-β signaling inhibited fibrosis in mouse models in vivo as well as in patient-derived liver spheroids. The CC regulates TGF-β signaling, and the breakdown of this control is associated with liver fibrosis in patients. Pharmacological proof-of-concept studies across different models have uncovered the CC as a novel therapeutic target for liver fibrosis – a growing unmet medical need. Liver fibrosis due to metabolic diseases is a global health challenge. Many liver functions are rhythmic throughout the day, being controlled by the circadian clock (CC). Here we demonstrate that regulation of the CC is perturbed upon chronic liver injury and this perturbation contributes to fibrotic disease. By showing that a compound targeting the CC improves liver fibrosis in patient-derived models, this study provides a novel therapeutic candidate strategy to treat fibrosis in patients. Additional studies will be needed for clinical translation. Since the findings uncover a previously undiscovered profibrotic mechanism and therapeutic target, the study is of interest for scientists investigating liver disease, clinical hepatologists and drug developers. [Display omitted] • The circadian clock is a regulator of TGF-β signaling in the healthy liver. • The breakdown of circadian clock control in MASH is associated with liver fibrosis progression. • Proof-of-concept studies in several models unravel targetability by a small molecule. • Pharmacological targeting of the circadian clock provides opportunities to improve liver fibrosis. [ABSTRACT FROM AUTHOR]

Isoprenoids comprise the largest group of plant specialized metabolites. 1‐deoxy‐D‐xylulose‐5‐phosphate synthase (DXS) is one of the major rate‐limiting enzymes in their biosynthesis. The DXS family expanded structurally and functionally during evolution and is believed to have significantly contributed to metabolic complexity and diversity in plants. This family has not yet been studied in Physcomitrium patens or other bryophytes.Here, we assessed the degree of evolutionary expansion in the DXS family in bryophytes and, more specifically, in P. patens using phylogenetic analysis. Transcriptome profiling was applied to investigate tissue‐specific, developmental, and environmental responses, such as salt stress, in the DXS family. Moreover, the effect of salt stress on terpenoid biosynthesis was monitored through metabolomics.The phylogenetic analysis of DXS revealed that a structural expansion occurred in bryophytes, but not in P. patens. Functional complementation assay revealed functional activity in all four copies. Comparative transcriptomics showed tissue‐ and condition‐specific divergence in the expression profiles of DXS copies and demonstrated specific stress responses for PpDXS1D, particularly to salt stress. These findings coincide with increased flux in the pathway towards downstream metabolites under salt stress. Additionally, co‐expression network analysis revealed significant differences between the co‐expressed genes of the DXS copies and illustrated enrichment of stress‐responsive genes in the PpDXS1D network.These results suggest that the DXS family in P. patens is conserved but undergoes differential transcriptional regulation, which might allow P. patens to fine‐tune DXS levels under different conditions, such as abiotic stress. [ABSTRACT FROM AUTHOR]

We modelled and calibrated the distributions of the seven-stripe patterns of Even-skipped (Eve) and Fushi-tarazu (Ftz) pair-rule proteins along the anteroposterior axis of the Drosphila embryo, established during early development. We have identified the putative repressive combinations for five Eve enhancers, and we have explored the relationship between Eve and Ftz for complementary patterns. The regulators of Eve and Ftz are stripe-specific DNA enhancers with embryo position-dependent activation rates and are regulated by the gap family of proteins. We achieved remarkable data matching of the Eve stripe pattern, and the calibrated model reproduces gap gene mutation experiments. Extended work inferring the Wingless (Wg) fourteen stripe pattern from Eve and Ftz enhancers have been proposed, clarifying the hierarchical structure of Drosphila 's genetic expression network during early development. [Display omitted] • We modelled seven stripe-specific enhancers for eve with the mass-action law describing transcriptional regulation. • We identified two gap repressive combinations driving ftz enhancers achieving Ftz's pattern, except stripe 4. • We model the fourteen-stripe pattern of Wingless from Eve and Ftz repressive transcription factors. [ABSTRACT FROM AUTHOR]

Chromatin is dynamically regulated during development, where structural changes affect the transcription of genes required to promote different cell types. One of the chromatin regulatory factors responsible for transcriptional regulation during development is the SWItch/Sucrose Non-Fermentable (SWI/SNF) complex, an ATP-dependent chromatin remodeling factor conserved throughout eukaryotes. The catalytic subunit of this complex, BRG1, is shared in all three SWI/SNF complexes subfamilies and is essential for developing most cell lineages. Interestingly, many human developmental diseases have correlative or causative mutations in different SWI/SNF subunits. Many polybromo-associated BAF (pBAF) complex-specific subunit genetic alterations result in developmental failures in tissue-specific ways. This observation suggests that the pBAF complex plays a vital role in development and differentiation, and studying the pBAF complex may provide an opportunity to better understand gene regulation during development. In this mini-view, we will focus on the functions of pBAF-specific subunits and their influence on the development of various cell and tissue types by regulating developmental gene expression. [ABSTRACT FROM AUTHOR]

Proline biosynthesis and catabolism pathways are executed by powerful action of specific enzymes that are subjected to environmental fluctuations at the transcriptional level. Previous researches have demonstrated that osmotic stress-induced upstream events can affect the expression of proline metabolism-related genes, which results in adjustable free proline accumulation to protect plant cells from severe damage. Here, we mainly describe the mechanisms for how some key factors, such as transcription factors, ABA (abscisic acid), Ca2+, MAPK cascades, CK (cytokinin) and phospholipase, in a phosphorylated manner, vividly function in the transcriptional regulation of proline metabolism under osmotic stress. These mechanisms reveal that sustaining of proline homeostasis is an efficient way for plants to adapt to osmotic stress. • Involvement of the key genes related to proline metabolism affects plant tolerance to osmotic stress. • Mechanisms of ABA-dependent and ABA-independent synergistically regulate proline biosynthesis during osmotic stress. • Phosphorylation is a main theme of the relay of osmotic stress-induced signals involved in proline metabolism. • ABA signaling overrides cytokinin signaling as a result of the inhibition of ProDH1 transcription upon the exposure of osmotic stress. [ABSTRACT FROM AUTHOR]