Gene Transcriptional Activity Research Articles

A novel three-layer module BoMYB1R1-BoMYB4b/BoMIEL1-BoDFR1 regulates anthocyanin accumulation in kale.

Anthocyanin is an important pigment responsible for plant coloration and beneficial to human health. Kale (Brassica oleracea var. acephala), a primary cool-season flowers and vegetables, is an ideal material to study anthocyanin biosynthesis and regulation mechanisms due to its anthocyanin-rich leaves. However, the underlying molecular mechanism of anthocyanin accumulation in kale remains poorly understood. Previously, we demonstrated that BoDFR1 is a key gene controlling anthocyanin biosynthesis in kale. Here, we discovered a 369-bp InDel variation in the BoDFR1 promoter between the two kale inbred lines with different pink coloration, which resulted in reduced transcriptional activity of the BoDFR1 gene in the light-pink line. With the 369-bp insertion as a bait, an R2R3-MYB repressor BoMYB4b was identified using the yeast one-hybrid screening. Knockdown of the BoMYB4b gene led to increased BoDFR1 expression and anthocyanin accumulation. An E3 ubiquitin ligase, BoMIEL1, was found to mediate the degradation of BoMYB4b, thereby promoting anthocyanin biosynthesis. Furthermore, the expression level of BoMYB4b was significantly reduced by light signals, which was attributed to the direct repression of the light-signaling factor BoMYB1R1 on the BoMYB4b promoter. Our study revealed that a novel regulatory module comprising BoMYB1R1, BoMIEL1, BoMYB4b, and BoDFR1 finely regulates anthocyanin accumulation in kale. The findings aim to establish a scientific foundation for genetic improvement of leaf color traits in kale, meanwhile, providing a reference for plant coloration studies.

Epigenetic underpinnings of the autistic mind: Histone modifications and prefrontal excitation/inhibition imbalance.

Autism spectrum disorder (ASD) is complex neurobehavioral condition influenced by several cellular and molecular mechanisms that are often concerned with synaptogenesis and synaptic activity. Based on the excitation/inhibition (E/I) imbalance theory, ASD could be the result of disruption in excitatory and inhibitory synaptic transmission across the brain. The prefrontal cortex (PFC) is the chief regulator of executive function and can be affected by altered neuronal excitation and inhibition in the course of ASD. The molecular mechanisms involved in E/I imbalance are subject to epigenetic regulation. In ASD, altered enrichment and spreading of histone H3 and H4 modifications such as the activation-linked H3K4me2/3, H3K9ac, and H3K27ac, and repression-linked H3K9me2, H3K27me3, and H4K20me2 in the PFC result in dysregulation of molecules mediating synaptic excitation (ARC, EGR1, mGluR2, mGluR3, GluN2A, and GluN2B) and synaptic inhibition (BSN, EphA7, SLC6A1). Histone modifications are a dynamic component of the epigenetic regulatory elements with a pronounced effect on patterns of gene expression with regards to any biological process. The excitation/inhibition imbalance associated with ASD is based on the excitatory and inhibitory synaptic activity in different regions of the brain, including the PFC, the ultimate outcome of which is highly influenced by transcriptional activity of relevant genes.

METTL3 promotes the osteogenic differentiation of human periodontal ligament cells by increasing YAP activity via IGF2BP1 and YTHDF1-mediated m6A modification.

N6-Methyladenosine (m6A) has been confirmed to play a dynamic role in osteoporosis and bone metabolism. However, whether m6A is involved in the osteogenic differentiation of human periodontal ligament cells (hPDLCs) remains unclear. The present study aimed to verify the role of methyltransferase-like 3 (METTL3)-mediated m6A modification in the osteogenic differentiation of hPDLCs. The METTL3, Runx2, Osx, and YAP mRNA expression was determined by qPCR. METTL3, RUNX2, OSX, YTHDF1, YAP, IGF2BP1, and eIF3a protein expression was measured by Western blotting and immunofluorescence assays. The levels of m6A modification were evaluated by methylated RNA immunoprecipitation (MeRIP) and dot blot analyses. MeRIP-seq and RNA-seq were used to screen potential candidate genes. Nucleic acid and protein interactions were detected by immunoprecipitation. Alizarin red staining was used to evaluate the osteogenic differentiation of hPDLCs. Gene transcription and promoter activities were assessed by luciferase reporter assays (n ≥ 3). The expression of METTL3 and m6A modifications increased synchronously with the osteogenic differentiation of hPDLCs (p = .0016). YAP was a candidate gene identified by MeRIP-seq and RNA-seq, and its mRNA and protein expression levels were simultaneously increased. METTL3 increased the m6A methylated IGF2BP1-mediated stability of YAP mRNA (p = .0037), which in turn promoted osteogenic differentiation (p = .0147). Furthermore, METTL3 increased the translation efficiency of YAP by recruiting YTHDF1 and eIF3a to the translation initiation complex (p = .0154), thereby promoting the osteogenic differentiation of hPDLCs (p = .0012). Our study revealed that METTL3-initiated m6A mRNA methylation promotes osteogenic differentiation of hPDLCs by increasing IGF2BP1-mediated YAP mRNA stability and recruiting YTHDF1 and eIF3a to the translation initiation complex to increase YAP mRNA translation. Our findings reveal the mechanism of METTL3-mediated m6A modification during hPDLC osteogenesis, providing a potential therapeutic target for periodontitis and alveolar bone defects.

Tissue expression and promoter activity analysis of the porcine TNFSF11 gene

Tumour necrosis factor (TNF) superfamily member 11 (TNFSF11), also known as RANKL, plays a crucial role in regulating several physiological and pathological activities. Additionally, it is a vital factor in bone physiology, and the sex hormone progesterone regulates the expansion of stem cells and the proliferation of mammary epithelial cells. It is essential for animal growth and reproductive physiological processes. This study aimed to evaluate the tissue-specific expression characteristics and promoter activity of the TNFSF11 gene in pigs. As a result, the study examined the presence of TNFSF11 expression in the tissues of Xiangsu pigs at 0.6 and 12 months of age. Moreover, the core promoter region of TNFSF11 was also identified by utilizing a combination of bioinformatic prediction and dual-luciferase activity tests. Finally, the effect of transcription factors on the transcriptional activity of the core promoter region was determined using site-directed mutagenesis. TNFSF11 was uniformly expressed in all tissues; however, its expression in muscles was comparatively low. The core promoter region of TNFSF11 was located in the -555 to -1 region. The prediction of the transcription start site of TNFSF11 gene-2000 ∼ + 500bp showed that there was a CpG site in 17 ∼ + 487bp. Analysis of mutations in the transcription factor binding sites revealed that mutations in the Stat5b, Myog, Trl, and EN1 binding sites had significant effects on the transcriptional activity of the TNFSF11 gene, particularly following the EN1 binding site mutation (P < 0.001). This study provides insights into both the tissue-specific expression patterns of TNFSF11 in the tissues of Xiangsu pigs and the potential regulatory effects of transcription factors on its promoter activity. These results may be helpful for future research aimed at clarifying the expression and role of the porcine TNFSF11 gene.

An evolutionary view of CC-type glutaredoxins functions in land plants development and adaptation to environment.

Land plants have to face an oxidizing, heterogeneous and fast changing environment. Redox-dependent post-translational modifications emerge as a critical component of plant responses to stresses. Among thiols oxidoreductases superfamily, class III CC-type glutaredoxins (called ROXYs) are land plant specific, and their evolutionary history is highly dynamic. Angiosperms encode many isoforms classified into five subgroups (Aα, Aβ, Bα, Bβ, Bγ) that probably evolved from five common ancestral ROXYs, with higher evolutionary dynamics in Bγ compared to other subgroups. ROXYs can modulate the transcriptional activity of TGAs transcription factors target genes, although their biochemical function is still debated. ROXYs participate in the control of proper plant development and reproduction, and are mainly negative regulators of plant responses to biotic and abiotic stresses. This suggests that most ROXYs could play essential and conserved functions in resetting redox-dependent changes in transcriptional activity upon stress signaling to ensure the responsiveness of the system and/or avoid exaggerated responses that could lead to major defects in plant growth and reproduction. Bγ members in Arabidopsis acquired important functions in responses to nitrogen availability and endogenous status, but the rapid and independent evolution of this subclass could suggest that this function results from neofunctionalization, specifically observed in core Eudicots.

Exogenous Cytokinin 4PU-30 Modulates the Response of Wheat and Einkorn Seedlings to Ultraviolet B Radiation.

Abiotic stress is responsible for a significant reduction in crop plant productivity worldwide. Ultraviolet (UV) radiation is a natural component of sunlight and a permanent environmental stimulus. This study investigated the distinct responses of young wheat and einkorn plants to excessive UV-B radiation (180 min at λmax 312 nm) following foliar pretreatment with 1 µM synthetic cytokinin 4PU-30. Results demonstrated that UV radiation significantly amplified hydrogen peroxide levels in both wheat and einkorn, with einkorn exhibiting a more pronounced increase compared to wheat. This elevation indicated the induction of oxidative stress by UV radiation in the two genotypes. Intensified antioxidant enzyme activities and the increased accumulation of typical stress markers and non-enzyme protectants were evidenced. Transcriptional activity of genes encoding the key antioxidant enzymes POX, GST, CAT, and SOD was also investigated to shed some light on their genetic regulation in both wheat and einkorn seedlings. Our results suggested a role for POX1 and POX7 genes in the UV-B tolerance of the two wheat species as well as a cytokinin-stimulated UV-B stress response in einkorn involving the upregulation of the tau subfamily gene GSTU6. Based on all our findings, it could be concluded that 4PU-30 had the potential of alleviating oxidative stress by attenuating the symptoms of superfluous UV-B illumination in the two examined plant species.

A time-resolved multi-omics atlas of transcriptional regulation in response to high-altitude hypoxia across whole-body tissues

High-altitude hypoxia acclimatization requires whole-body physiological regulation in highland immigrants, but the underlying genetic mechanism has not been clarified. Here we use sheep as an animal model for low-to-high altitude translocation. We generate multi-omics data including whole-genome sequences, time-resolved bulk RNA-Seq, ATAC-Seq and single-cell RNA-Seq from multiple tissues as well as phenotypic data from 20 bio-indicators. We characterize transcriptional changes of all genes in each tissue, and examine multi-tissue temporal dynamics and transcriptional interactions among genes. Particularly, we identify critical functional genes regulating the short response to hypoxia in each tissue (e.g., PARG in the cerebellum and HMOX1 in the colon). We further identify TAD-constrained cis-regulatory elements, which suppress the transcriptional activity of most genes under hypoxia. Phenotypic and transcriptional evidence indicate that antenatal hypoxia could improve hypoxia tolerance in offspring. Furthermore, we provide time-series expression data of candidate genes associated with human mountain sickness (e.g., BMPR2) and high-altitude adaptation (e.g., HIF1A). Our study provides valuable resources and insights for future hypoxia-related studies in mammals.

CpSmt3, an ortholog of small ubiquitin-like modifier, is essential for growth, organelle function, virulence, and antiviral defense in Cryphonectria parasitica.

SUMOylation is an important post-translational modification that regulates the expression, localization, and activity of substrate proteins, thereby participating in various important cellular processes such as the cell cycle, cell metabolism, gene transcription, and antiviral activity. However, the function of SUMOylation in phytopathogenic fungi has not yet been adequately explored. A comprehensive analysis composed of proteomics, affinity pull-down, molecular and cellular approaches was performed to explore the roles of SUMOylation in Cryphonectria parasitica, the fungal pathogen responsible for chestnut blight. CpSmt3, the gene encoding the SUMO protein CpSmt3 in C. parasitica was identified and characterized. Deletion of the CpSmt3 gene resulted in defects in mycelial growth and hyphal morphology, suppression of sporulation, attenuation of virulence, weakening of stress tolerance, and elevated accumulation of hypovirus dsRNA. The ΔCpSmt3 deletion mutant exhibited an increase in mitochondrial ROS, swollen mitochondria, excess autophagy, and thickened cell walls. About 500 putative SUMO substrate proteins were identified by affinity pull-down, among which many were implicated in the cell cycle, ribosome, translation, and virulence. Proteomics and SUMO substrate analyses further revealed that deletion of CpSmt3 reduced the accumulation of CpRho1, an important protein that is involved in TOR signal transduction. Silencing of CpRho1 resulted in a phenotype similar to that of ΔCpSmt3, while overexpression of CpRho1 could partly rescue some of the prominent defects in ΔCpSmt3. Together, these findings demonstrate that SUMOylation by CpSmt3 is vitally important and provide new insights into the SUMOylation-related regulatory mechanisms in C. parasitica.

MYB4 is the best candidate transcription factor involved in pinosylvin stilbene biosynthesis in Pinus strobus L. cells by fungal elicitor treatment

Key messageDihydropinosylvin monomethyl ether (DPME) and pinosylvin monomethyl ether (PME) are pinosylvin derivatives that show high nematicidal activity against pine wood nematodes (PWNs). Here, we found that fungal elicitor treatment boosted the production of DPME and PME in cultured Pinus strobus L. cells and investigated the transcription factors (TFs) regulating the genes in the pinosylvin stilbenoid biosynthesis pathway.ContextThe discovery of TFs involved in the synthesis of DPME and PME provides an important clue to understanding the pinosylvin stilbenoid synthesis in pine plants.AimsWe investigated the best fungal elicitor for the production of DPME and PME and the transcriptional activities of genes involved in PME and DPME biosynthesis in P. strobus L. cells after fungal elicitor treatment.MethodsThe content of DPME and PME in P. strobus cells was examined after treatment with fungal elicitors prepared from seven different species of fungi. Moreover, the role of fungal elicitors in the transcriptional activity of genes involved in DPME and PME biosynthesis was investigated by transcriptome analysis using RNA sequencing.ResultsPenicillium chrysogenum Thorn was the most efficient fungal elicitor for the production of DPME and PME in P. strobus cells among the other fungal species. The accumulation of DPME and PME in P. strobus cells after P. chrysogenum elicitor treatment increased 12.7-fold and 23.7-fold, respectively, compared to the control. Transcriptome analysis revealed that fungal elicitor treatment resulted in enhanced transcription of the PAL, 4CL, STS, PMT, and ACC genes, which are involved in PME and DPME biosynthesis. Some transcription factors belonging to the bHLH, MYB, WRKY, and ERF families showed a high transcription rate after fungal elicitor treatment.ConclusionsWe found that the fungal elicitor is a strong inducer of the accumulation of pinosylvin derivatives in the cells of P. strobus. We selected one unigene (c133966_g3_i1 in the MYB family) as the best candidate TF that regulates the DPME and PME biosynthesis in P. strobus by transcriptome analysis.

High histone crotonylation modification in bovine fibroblasts promotes cell proliferation and the developmental efficiency of preimplantation nuclear transfer embryos

Lysine crotonylation (Kcr) is a recently discovered histone acylation modification that is closely associated with gene expression, cell proliferation, and the maintenance of stem cell pluripotency and indicates the transcriptional activity of genes and the regulation of various biological processes. During cell culture, the introduction of exogenous croconic acid disodium salt (Nacr) has been shown to modulate intracellular Kcr levels. Although research on Kcr has increased, its role in cell growth and proliferation and its potential regulatory mechanisms remain unclear compared to those of histone methylation and acetylation. Our investigation demonstrated that the addition of 5 mM Nacr to cultured bovine fibroblasts increased the expression of genes associated with Kcr modification, ultimately promoting cell growth and stimulating cell proliferation. Somatic cell nuclear transfer of donor cells cultured in 5 mM Nacr resulted in 38.1% blastocyst development, which was significantly greater than that in the control group (25.2%). This research is important for elucidating the crotonylation modification mechanism in fibroblast proliferation to promote the efficacy of somatic cell nuclear transfer.

Overexpression of ZNF169 promotes the growth and proliferation of colorectal cancer cells via the upregulation of ANKZF1.

Colorectal cancer (CRC) is one of the most common malignancies worldwide. The 5‑year survival rate of patients diagnosed with the early stages of the disease is markedly higher than that of patients in the advanced stages. Therefore, identifying novel biomarkers and drug targets for CRC is critical for clinical practice. Zinc finger protein 169 (ZNF169) is a crucial transcription factor, and its role in CRC remains to be explored. The present study aimed to investigate the clinical relevance, function and underlying mechanisms of ZNF169 in CRC growth and proliferation. The Cancer Genome Atlas (TCGA) database was utilized to analyze the clinical relevance of ZNF169 in patients with CRC. Immunohistochemical staining was performed on tissue samples from patients with CRC to detect the expression of ZNF169. The HCT‑116, HT‑29 and RKO cell lines were employed for in vitro experiments. The overexpression and knockdown of ZNF169 were achieved by transfecting the cells with lentivirus and small interfering RNAs, respectively. Cell Counting Kit‑8, colony formation and EdU staining assays were applied to investigate the function of ZNF169 in CRC cells. Dual luciferase activity and chromatin immunoprecipitation (ChIP)‑quantitative PCR (qPCR) assays were performed to identify the regulatory effects of ZNF169 on the ankyrin repeat and zinc‑finger domain‑containing 1 (ANKZF1; also known as ZNF744) gene. Reverse transcription‑quantitative PCR and western blot analysis were performed to measure mRNA and protein expression, respectively. The analysis of TCGA data revealed a positive correlation between ZNF169 and ANKZF1, with the overexpression of ANKZF1 being associated with a poor prognosis of patients with CRC. The experimental results demonstrated that ZNF169 was expression upregulated in CRC tissue compared with that in normal colon tissue. Gain‑of‑function and loss‑of‑function experiments revealed that ZNF169 enhanced the intensity of EdU staining, promoting the growth and proliferation of CRC cells. Furthermore, the overexpression of ZNF169 potentiated the transcriptional activity of the ANKZF1 gene, while the knockdown of ZNF169 produced the opposite results. ChIP‑qPCR confirmed the interaction between ZNF169 and the promoter sequence of ANKZF1. Rescue experiments revealed that ZNF169 accelerated CRC cell growth and proliferation through the upregulation of ANKZF1. Furthermore, there was a positive correlation identified between ZNF169 and ANKZF1, and upregulation of ANKZF1 expression was associated with the poor prognosis of patients with CRC. On the whole, the present study demonstrates that ZNF169 contributes to CRC malignancy by potentiating the expression of ANKZF1. Thus, the regulation of ZNF169 and/or ANKZF1 expression may represent a viable strategy for the treatment patients with CRC with a high expression of ZNF169.

Adaptive expansion of ERVK solo-LTRs is associated with Passeriformes speciation events

Endogenous retroviruses (ERVs) are ancient retroviral remnants integrated in host genomes, and commonly deleted through unequal homologous recombination, leaving solitary long terminal repeats (solo-LTRs). This study, analysing the genomes of 362 bird species and their reptilian and mammalian outgroups, reveals an unusually higher level of solo-LTRs formation in birds, indicating evolutionary forces might have purged ERVs during evolution. Strikingly in the order Passeriformes, and especially the parvorder Passerida, endogenous retrovirus K (ERVK) solo-LTRs showed bursts of formation and recurrent accumulations coinciding with speciation events over past 22 million years. Moreover, our results indicate that the ongoing expansion of ERVK solo-LTRs in these bird species, marked by high transcriptional activity of ERVK retroviral genes in reproductive organs, caused variation of solo-LTRs between individual zebra finches. We experimentally demonstrated that cis-regulatory activity of recently evolved ERVK solo-LTRs may significantly increase the expression level of ITGA2 in the brain of zebra finches compared to chickens. These findings suggest that ERVK solo-LTRs expansion may introduce novel genomic sequences acting as cis-regulatory elements and contribute to adaptive evolution. Overall, our results underscore that the residual sequences of ancient retroviruses could influence the adaptive diversification of species by regulating host gene expression.

GSK0660 enhances antitumor immunotherapy by reducing PD-L1 expression

Blockade of PD-1/PD-L1 immune checkpoint is wildly used for multiple types of cancer treatment, while the low response rate for patients is still completely unknown. As nuclear hormone receptor, PPARδ (peroxisome-proliferator-activated receptor) regulates cell proliferation, inflammation, and tumor progression, while the effect of PPARδ on tumor immune escape is still unclear. Here we found that PPARδ antagonist GSK0660 significantly reduced colon cancer cell PD-L1 protein and gene expression. Luciferase analysis showed that GSK0660 decreased PD-L1 gene transcription activity. Moreover, reduced PD-L1 expression in colon cancer cells led to increased T cell activity. Further analysis showed that GSK0660 decreased PD-L1 expression in a PPARδ dependent manner. Implanted tumor model analysis showed that GSK0660 inhibited tumor immune escape and the combined PD-1 antibody with GSK0660 effectively enhanced colorectal cancer immunotherapy. These findings suggest that GSK0660 treatment could be an effective strategy for cancer immunotherapy.

Abstract 963: Comprehensive epigenomic profiling from plasma to inform therapy selection: A proof-of-concept study in cancer

Abstract BACKGROUND: Analysis of genomic alterations in circulating tumor DNA is gaining traction in clinical oncology and can provide insights into tumor biology without the need for invasive tissue sampling. In addition to genetic alterations, epigenomic reprogramming leads to transcriptional dysregulation and drives cancer phenotypes including molecular subtypes, histologic subtypes, and mechanisms resistance. As current liquid biopsy assays fail to effectively capture transcriptional biology, new approaches are needed to examine the transcriptional status of therapeutic gene targets and pathways including those relevant to rapidly emerging classes such as antibody-drug conjugates (ADC) and radio-conjugates. METHODS: We developed a novel multimodal assay that reveals genome-wide transcriptional activity of promoters, enhancers from chromatin and surveys the DNA methylome using 1ml of patient plasma. We applied this assay to patient plasma samples from across 15 tumor types generating 7000 genome-wide transcriptional profiles. RESULTS: We confirmed a significant correlation between epigenomic signals of transcriptional activation and gene expression from RNA-seq (Promoter vs RNA-seq: ⍴ =0.95, p&amp;lt;0.05; DNA methylation vs RNA-seq: ⍴=-0.16, p&amp;lt;0.05). We identified transcriptional activation in cancer patient plasma of well-established cancer-associated biomarkers (e.g. MET, DLL3, PSMA) in a tumor-specific manner. Epigenomic profiling simultaneously inferred the expression of multiple pertinent ADC targets currently under investigation (MET, HER2, HER3, TROP2, B7H4 in breast cancer), and SLFN11, a known biomarker for sensitivity to these agents. Unlike targeted panels, the platform assesses transcriptional regulation genome-wide, enabling the assessment of transcriptional activity of select genes as well as related pathways. For example, a multimodal classifier robustly predicted HER2 status across metastatic breast cancer plasma samples based on features both within the HER2 amplicon as well as HER2-distal genes that are activated in HER2+ cancers (AUC = 0.93, 0.84-1.0 95% CI). The multimodal classifier out-performed individual analyte-based classifiers (AUCPromoter+Enhancer = 0.85, 0.72-0.98 95% CI; AUCDNA-methylation = 0.69, 0.48-0.90 95% CI). Epigenomic signatures were also used to delineate multiple mechanisms of resistance to androgen receptor signaling inhibition in prostate cancer, including reactivation of the androgen receptor, glucocorticoid signaling bypass, and histological transformation to a neuroendocrine subtype. CONCLUSION: This comprehensive epigenomic liquid biopsy assay provides a platform for simultaneous genome-wide transcriptional assessment of disease and therapy relevant genes and pathways, representing a paradigm shift in our ability to longitudinally monitor cancer in individual patients. Citation Format: Travis Clark, Ji-Heui Seo, Anthony D'Ippolito, Aparna Gorthi, Jonathan Beagan, Jamey Guess, Amy Donahue, Mandy Greene, Alyssa Lau, Fernando Ramirez, Kristian Cibulskis, Hyun-Hwan Jeong, Matthew Davidsohn, Gitanjali Lakshminarayanam, Michael Coyne, Baovy Tran, Tyrone Tamakloe, Hathairat Sawaengsri, Marc Eid, Karl Semaan, Brad Fortunato, Corrie A. Painter, Juliann Chmielecki, Toni K. Choueiri, J Carl Barrett, Geoff Otto, Matthew L. Freedman, Matthew L. Eaton, Sylvan C. Baca. Comprehensive epigenomic profiling from plasma to inform therapy selection: A proof-of-concept study in cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 963.

Effect of chronic intake of cadmium chloride on the transcriptional activity of metallothionein and zinc transporter genes

Introduction. Cadmium chloride is an inorganic compound containing cadmium, a heavy metal that is one of the active environmental pollutants today. Damage to organs in experimental animals due to cadmium poisoning is similar to that in humans. In this work, the activity of metallothionein and zinc transporters genes was studied in a chronic model of cadmium-induced poisoning in experimental animals.&#x0D; Materials and methods. The experiment was carried out using seventy two individuals of white inbred rats of both sexes, the average weight of which was 215 g. Animals from four groups were injected with a solution of cadmium chloride in four different doses, respectively, individuals of the fifth group, the control group, received an equimolar volume of pure water. The objects of the study were the kidneys and livers of rats, removed after the animals were withdrawn from the experiment. Next, the activity of the Mt1A, Mt2A, Mt3A, Zip1 and Znt1 genes was analyzed in organ samples using real-time PCR.&#x0D; Results. Significant increases in the expression multiplicity of Mt1A, Mt2A and Mt3A metallothionein genes in the kidneys at different doses of the toxicant were revealed. In liver samples, a decrease in the expression of the Mt2A gene was found in the experimental group exposed to cadmium chloride at a dose &#x0D; of 0.1 mg/kg (p&lt;0.05). For the Znt1 gene in rat liver tissue, there was a statistically significant decrease in expression at a dose of 0.001 mg/kg (p&lt;0.05) &#x0D; and, conversely, an increase at doses of 0.1 and 1 mg/kg (p&lt;0.05) compared to the control group. Analysis of the level of transcripts of the Zip1 gene in the kidneys and liver after 6 months of inoculation with the toxicant in the presented doses did not reveal statistically significant differences between the groups.&#x0D; Limitations. Laboratory animals of the only biological species were used for the experiment. Four doses of the cadmium salt alone were evaluated.&#x0D; Conclusion. The results obtained allow concluding that the level of expression of the Mt1A, Mt2A and Mt3A genes in the kidneys can play the role of a diagnostic marker in chronic poisoning with the toxicant under study.

An Imbalance in Histone Modifiers Induces tRNA-Cys-GCA Overexpression and tRF-27 Accumulation by Attenuating Promoter H3K27me3 in Primary Trastuzumab-Resistant Breast Cancer.

tRNA-derived fragments (tRFs) play crucial roles in cancer progression. Among them, tRF-27 has been identified as a key factor in promoting naïve trastuzumab resistance in HER2-positive breast cancer. However, the origin of tRF-27 remains uncertain. In this study, we propose that the upregulated expression of specific cysteine tRNAs may lead to the increased accumulation of tRF-27 in trastuzumab-resistant JIMT1 cells. Mechanistically, the reduced inhibitory H3K27me3 modification at the promoter regions of tRF-27-related tRNA genes in JIMT1 cells, potentially resulting from decreased EZH2 and increased KDM6A activity, may be a critical factor stimulating the transcriptional activity of these tRNA genes. Our research offers fresh insights into the mechanisms underlying elevated tRF-27 levels in trastuzumab-resistant breast cancer cells and suggests potential strategies to mitigate trastuzumab resistance in clinical treatments.

The influence of mitochondria-targeted antioxidants, plastoquinone derivatives on the resistance of grain crops to water deficiency

The article presents the results of a study of the influence of plastoquinone derivatives: 10-(6'-plastoquinonyl)decyltriphenylphosphonium (SkQ1) and 10-(6′-methylplastoquinonyl) decyltriphenylphosphonium (SkQ3) on the resistance of grain crops to soil moisture deficiency. The object of the study were seedlings of spring barley (Hordeum vulgare L.) cultivar “Sokol” and winter wheat (Triticum aestivum L.) cultivar “Kalym”. The growth rates of plants were studied for 14 days under normal conditions and with a lack of moisture, pre-treated with 2.5 nm solutions of SkQ1 and SkQ3. It has been shown that treating seeds with solutions of SkQ1 and SkQ3 increases the growth rate of the studied crops under conditions of lack of moisture compared to the control. Also, in the roots and leaves of 14-day-old barley seedlings, an analysis of the transcriptional activity of the genes SodA1, SodB, GR, GST1, GST6, Cat1, Cat2, Apx1, encoding oxidative stress proteins, was carried out. It was shown that a decrease in soil moisture by 1.8 and 2.0 times compared to the control reduces to varying degrees the weight of roots and leaves in 14-day-old barley seedlings and increases the transcriptional activity of all studied genes in both leaves and roots. Treatment of seeds with solutions of SkQ1 and SkQ3 under conditions of moisture deficiency increases the dry weight of barley roots and leaves and reduces the transcriptional activity of the studied genes in the roots. Keywords: PLASTOQUINONE DERIVATIVES, SkQ1, SkQ3, MITOCHONDRIA-TARGETED ANTIOXIDANTS, ROS, SOIL MOISTURE DEFICIENCY, STABILITY, TRANSCRIPTIONAL GENE ACTIVITY

The landscape of transcription factor promoter activity during vegetative development in Marchantia.

Transcription factors (TFs) are essential for the regulation of gene expression and cell fate determination. Characterizing the transcriptional activity of TF genes in space and time is a critical step toward understanding complex biological systems. The vegetative gametophyte meristems of bryophytes share some characteristics with the shoot apical meristems of flowering plants. However, the identity and expression profiles of TFs associated with gametophyte organization are largely unknown. With only ∼450 putative TF genes, Marchantia (Marchantia polymorpha) is an outstanding model system for plant systems biology. We have generated a near-complete collection of promoter elements derived from Marchantia TF genes. We experimentally tested reporter fusions for all the TF promoters in the collection and systematically analyzed expression patterns in Marchantia gemmae. This allowed us to build a map of expression domains in early vegetative development and identify a set of TF-derived promoters that are active in the stem-cell zone. The cell markers provide additional tools and insight into the dynamic regulation of the gametophytic meristem and its evolution. In addition, we provide an online database of expression patterns for all promoters in the collection. We expect that these promoter elements will be useful for cell-type-specific expression, synthetic biology applications, and functional genomics.

CENPA promotes glutamine metabolism and tumor progression by up-regulating SLC38A1 in endometrial cancer

Glutamine addiction is a significant hallmark of metabolic reprogramming in tumors and is crucial to the progression of cancer. Nevertheless, the regulatory mechanisms of glutamine metabolism in endometrial cancer (EC) remains elusive. In this research, we found that elevated expression of CENPA and solute carrier family 38 member 1 (SLC38A1) were firmly associated with worse clinical stage and unfavorable outcomes in EC patients. In addition, ectopic overexpression or silencing of CENPA could either enhance or diminish glutamine metabolism and tumor progression in EC. Mechanistically, CENPA directly regulated the transcriptional activity of the target gene, SLC38A1, leading to enhanced glutamine uptake and metabolism, thereby promoting EC progression. Notably, a prognostic model utilizing the expression levels of CENPA and SLC38A1 genes independently emerged as a prognostic factor for EC. More importantly, CENPA and SLC38A1 were significantly elevated and positively correlated, as well as indicative of poor prognosis in multiple cancers. In brief, our study confirmed that CENPA is a critical transcription factor involved in glutamine metabolism and tumor progression through modulating SLC38A1. This revelation suggests that targeting CENPA could be an appealing therapeutic approach to address pan-cancer glutamine addiction.

Investigating the Role of OrbF in Biofilm Biosynthesis and Regulation of Biofilm-Associated Genes in Bacillus cereus BC1.

Bacillus cereus (B. cereus), a prevalent foodborne pathogen, constitutes a substantial risk to food safety due to its pronounced resilience under adverse environmental conditions such as elevated temperatures and ultraviolet radiation. This resilience can be attributed to its capacity for biofilm synthesis and sustained high viability. Our research aimed to elucidate the mechanisms governing biofilm biosynthesis in B. cereus. To this end, we constructed a 5088-mutant library of the B. cereus strain BC1 utilizing the transposon TnYLB-1. Systematic screening of this library yielded mutants exhibiting diminished biofilm formation capabilities. Twenty-four genes associated with the biofilm synthesis were identified by reverse PCR in these mutants, notably revealing a significant reduction in biofilm synthesis upon disruption of the orbF gene in B. cereus BC1. Comparative analysis between the wild type and orbF-deficient BC1 strains (BC1ΔorbF) indicated a marked downregulation (decreased by 11.7% to 96.7%) in the expression of genes implicated in biofilm formation, flagellar assembly, and bacterial chemotaxis in the BC1ΔorbF. Electrophoretic mobility shift assay (EMSA) further corroborated the role of OrbF, demonstrating its binding to the promoter region of the biofilm gene cluster, subsequently leading to the suppression of transcriptional activity of biofilm-associated genes in B. cereus BC1. Our findings underscore the pivotal role of orbF in biofilm biosynthesis in B. cereus, highlighting its potential as a target for strategies aimed at mitigating biofilm formation in this pathogen.