Regulation Of Gene Transcription Research Articles

MGCN-PolyA: An Integrated Computational Framework for Predicting Poly(A) Signals with Multiscale-gated Convolutional Networks

Background: The accurate recognition of the polyadenylation signal (PAS) from DNA sequences is essential for understanding gene transcriptional regulation. A variety of machine learning-based computational methods have been developed to predict PAS in recent years; however, their performance and their generalization ability are unsatisfactory. It is highly desirable to design more preferable computational approaches for PAS prediction. Methods: In this work, we developed an integrated framework MGCN-PolyA for PAS prediction across four species, including Homo sapiens, Bos taurus, Mus musculus, and Drosophila melanogaster. MGCN-Poly(A) benefits from the diversity of feature engineering and the effectiveness of the model architecture. We combined features from different perspectives, such as word embedding, One-hot encoding, K-mer frequency, and Enhanced Nucleic Acid Composition (ENAC), which complement each other and provide rich and comprehensive information for model learning. In model architecture, MGCN-Poly(A) leverages a two-channel multi-scale gated convolutional network to effectively learn high-level feature representations at different scales, and then combines the statistical features to predict PAS using random forest algorithm. These designs not only speed up network training, but also improves the generalization ability Results: The benchmarking experiments on the independent test datasets demonstrate that MGCNPolyA outperforms other state-of-the-art algorithms in identifying PAS. MGCN-PolyA has the highest accuracy on all test datasets, and its excellent performance on cross-species validation also demonstrates the robustness of our model. Conclusion: Extracting features from different perspectives is important for PAS recognition, and the integration of DNNs and shallow machine learning algorithms can improve the model performance.

Role of lamin A/C on dendritic cell function in antiviral immunity

Dendritic cells (DCs) play a crucial role in orchestrating immune responses, particularly in promoting IFNγ-producing-CD8 cytotoxic T lymphocytes (CTLs) and IFNγ-producing-CD4 T helper 1 (Th1) cells, which are essential for defending against viral infections. Additionally, the nuclear envelope protein lamin A/C has been implicated in T cell immunity. Nevertheless, the intricate interplay between innate and adaptive immunity in response to viral infections, particularly the role of lamin A/C in DC functions within this context, remains poorly understood. In this study, we demonstrate that mice lacking lamin A/C in myeloid LysM promoter-expressing cells exhibit a reduced capacity to induce Th1 and CD8 CTL responses, leading to impaired clearance of acute primary Vaccinia virus (VACV) infection. Remarkably, in vitro-generated granulocyte macrophage colony-stimulating factor bone marrow-derived DCs (GM-CSF BMDCs) show high levels of lamin A/C. Lamin A/C absence on GM-CSF BMDCs does not affect the expression of costimulatory molecules on the cell membrane but it reduces the cellular ability to form immunological synapses with naïve CD4 T cells. Lamin A/C deletion induces alterations in NFκB nuclear localization, thereby influencing NF-κB-dependent transcription. Furthermore, lamin A/C ablation modifies the gene accessibility of BMDCs, predisposing these cells to mount a less effective antiviral response upon TLR stimulation. This study highlights the critical role of DCs in interacting with CD4 T cells during antiviral responses and proposes some mechanisms through which lamin A/C may modulate DC function via gene accessibility and transcriptional regulation.

Tumor suppressor BAP1 suppresses disulfidptosis through the regulation of SLC7A11 and NADPH levels

BAP1, BRCA1-Associated Protein 1, serves as a novel tumor suppressor through the deubiquitination of monoubiquitination of H2A and subsequent gene transcriptional regulation. Regulated cell death like apoptosis or ferroptosis is considered an essential mechanism mediating tumor suppression. Previous reports, including ours, have demonstrated that BAP1 could promote apoptosis and ferroptosis to inhibit tumor development. Whether BAP1 regulated additional types of cell death remains unclear. Disulfidptosis is a recently identified novel cell death mode characterized by aberrant accumulation of intracellular disulfide (e.g., cystine) and depletion of NADPH. In this study, we first demonstrated that BAP1 could significantly protect disulfidptosis induced by glucose starvation, which is validated by various cell death inhibitors and the accumulation of disulfide bonds in the cytoskeleton proteins. BAP1 is known to inhibit SLC7A11 expression. We found that the protective effect of BAP1 against disulfidptosis was counteracted when overexpressing SLC7A11 or adding additional cystine. Conversely, BAP1-mediated suppression of disulfidptosis was largely abrogated when SLC7A11-mediated cystine uptake was inhibited by the knockout of SLC7A11 or erastin treatment. Besides, high BAP1 expression showed lower NADP+/NADPH levels, which might confer resistance to disulfidptosis. Consistent with these observations, the expression level of BAP1 was also positively correlated with NADPH-related genes in KIRC patients, though the underlying mechanism mediating NADPH regulation remains further investigation. In summary, our results revealed the role of BAP1 in the regulation disulfidptosis and provided new insights into the understanding of disulfidptosis in tumor development.

Immune escape between endoplasmic reticulum stress-related cancer cells and exhausted CD8+T cells leads to neoadjuvant chemotherapy resistance in ovarian cancer

Our study aims to explore the effects of neoadjuvant chemotherapy (NACT) on tumour cells and immune cells in the immune microenvironment of patients with high-grade serous ovarian cancer (HGSOC).Single-cell RNA sequencing data of paired ovarian cancer tissues were analysed before and after NACT in 11 patients with HGSOC. The effect of NACT on two major cell components of the tumour microenvironment, epithelial cells and CD8+T cells, was investigated. The mechanisms of epithelial cell evasion by NACT and immune killing were explored from the perspectives of gene expression, functional characteristics, transcriptional regulation, and cell communication. Key targets for reversing NACT resistance were identified and possible therapeutic strategies proposed.While NACT improved the de novo differentiation of anti-tumour CD8+T cells, enhancing their anti-tumour function, it increased the proportion of cancer cells with high HSP90B1 expression. Thus, the potential reasons for NACT resistance were identified as: 1) high levels of endoplasmic reticulum stress (ERS) characteristics, 2) high expression of the MDK-NCL ligand-receptor pair between them and exhausted CD8+T cells before NACT, and 3) high expression of the NECTIN2-TIGIT immune ligand-receptor pair between them and exhausted CD8+T cells after NACT.Thus, our study reveals the mechanisms underlying NACT resistance in patients with HGSOC from the perspective of the independent and interactive roles of cancer cells and CD8+T cells. We propose therapeutic strategies targeting the ERS marker HSP90B1 and the immune escape marker MDK before or during NACT, while targeting NECTIN2 blockade after NACT. This approach may offer new insights into combination treatments for patients with HGSOC displaying NACT resistance.

Preparation, flavor component and antioxidant activity analysis of Lactiplantibacillus plantarum NCU137 fermented rice protein

Rice protein is the main component in the byproducts of rice processing such as rice dregs and rice bran. This study aims to develop lactic acid bacteria-fermented rice protein and analyze the changes of component and bioactivity. Lactiplantibacillus plantarum NCU137 was selected as the optimum fermentation strain from sixty lactic acid bacteria strains using fermentation performance and sensory score as the criteria. NCU137 was then applied to rice protein fermentation and the process parameters were optimized by single factor and orthogonal experiments. NCU137 fermentation significantly increased the acidity, antioxidant activity, and peptide content of rice protein, and eight volatile flavor compounds were identified as characteristic aroma components as determined by SPME-GC-MS. Of them, the OAV value of 1-hexanol was up to 50.94, contributing the most to the flavor of fermented rice protein. Furthermore, the antioxidant activity and mechanism of rice protein antioxidant peptide (RPAP) on H2O2-induced Caco-2 cell damage were investigated by CCK-8 method and fluorescence microscopy. RPAP showed protective effect on cell damage in a dose-dependent manner, accompanying by reduction of oxidative components such as ROS and MDA, and increasement of antioxidant components such as SOD, CAT, and GSH-PX. The protective effect might lie in the regulation of gene transcription in Nrf2/HO-1 and apoptosis Bax/Bcl pathway, as validated by RT-qPCR assay. Shortly, the rice protein fermented by NCU137 displayed significant improvement of flavor, nutritional components, and antioxidant bioactivity. The fermentation technology provides alternative strategy for processing rice protein in rice dregs and rice bran into high-valued products.

Calcitriol alleviates noise-induced hearing loss by regulating the ATF3/DUSP1 signalling pathway

BackgroundCalcitriol (Cal) is the most active metabolite of vitamin D and has antioxidant and anti-inflammatory properties. The aim of this study was to investigate the role of Cal in noise-induced hearing loss (NIHL) to further elucidate the mechanism of noise-induced oxidative stress in the mouse cochlea. MethodsC57BL/6 J mice were given six intraperitoneal injections of Cal (500 ng/kg/d). After 14 days of noise exposure, auditory brainstem response (ABR) thresholds, and the cochlear outer hair cell loss rate were analysed to evaluate auditory function. Real-time fluorescence quantitative PCR, immunofluorescence and western blotting were performed in vitro after the treatment of cochlear explants with 100 µM tert-butyl hydroperoxide (TBHP) for 2.5 h and HEI-OC1 cells with 250 µM TBHP for 1.5 h. ResultsIn vivo experiments confirmed that Cal pretreatment mitigated NIHL and outer hair cell death. The in vitro results demonstrated that Cal significantly reduced TBHP-induced cochlear auditory nerve fibre degradation and spiral ganglion neuron damage. Moreover, treatment with Cal inhibited the expression of oxidative stress-related factors (3-NT and 4-HNE) and DNA damage-related factors (γ-H2A.X) and attenuated TBHP-induced apoptosis in cochlear explants and HEI-OC1 cells. A total of 1479 upregulated genes and 1443 downregulated genes were screened in cochlear tissue 1 h after noise exposure. The level of transcription factor 3 (ATF3) was significantly elevated in HEI-OC1 cells after TBHP stimulation. Gene Transcription Regulation Database （GTRD）and Cistrome database analyses revealed that the downstream target gene of ATF3 is dual specificity phosphatase 1 (DUSP1). Cistrome DB Toolkit database results showed that the transcription factor of DUSP1 was ATF3. In addition, the ChIP-PCR results indicated that ATF3 might be a direct transcription factor of DUSP1. ConclusionThe results of our study suggest that Cal attenuates NIHL and inhibits noise-induced apoptosis by regulating the ATF3/DUSP1 signalling pathway.

Phenotypes of autism spectrum disorder and schizoaffective disorder associated with SETD1B gene but without intellectual disability and seizures.

The SETD1B gene, located on chromosome 12q24, is one of the chromatin-modifying genes involved in epigenetic regulation of gene transcription. The phenotype of pathogenic variants in the SETD1B gene includes intellectual disability, seizures, and language delay (IDDSELD, OMIM 619000). In this study, we present a family consisting of consanguineous parents who died of cancer and their offspring. This family includes two cases diagnosed with autism spectrum disorder (ASD); six cases diagnosed with schizophrenia, bipolar disorder, or schizoaffective disorder; there cases diagnosed with cancer; and five cases who died of unknown causes in early childhood. Three affected members of this family agreed to genetic testing. We used whole exome sequencing. We report a novel in-frame deletion variant of the SETD1B gene in a family with cases diagnosed with schizoaffective disorder and ASD without seizures and intellectual disability. It was found that the phenotypic features were inherited for at least three generations in the family we presented, and it was shown that the pathogenic variant of the SETD1B gene was transmitted from the affected parent to his affected children. In addition, the father was diagnosed with both schizoaffective disorder and leukemia. We proposed an association between rare variants of SETD1B and phenotypes of ASD and schizoaffective disorder without seizures and intellectual disability. The SETD1B gene is included in both the ASD genetic database of SFARI (https://gene.sfari.org/) and the cancer database of COSMIC (https://cancer.sanger.ac.uk/cosmic). However, there are very few reports of SETD1B gene variants as clinical entities. To our knowledge, the SETD1B gene variant has not been previously reported in an individual diagnosed with both a neuropsychiatric disorder and cancer.

Cyprinid herpesvirus 3 replication is inhibited via decreased ORF3 promoter activity mediated by multiple cellular transcription factors

Cyprinid herpesvirus 3 (CyHV-3) is an enveloped and double-stranded DNA virus that primarily infects common carp and its variants. The transcriptional regulation program of the viral immediate early (IE) genes plays a crucial role in virus replication. However, the transcriptional regulatory mechanism of CyHV-3 IE genes remains largely unclear. In this study, we found that the IE gene ORF3 promoter, which exhibited the highest activity among the eight CyHV-3 IE genes, was inhibited in the host common carp brain (CCB) cells. Deletions of the ORF3 promoter revealed the presence of multiple regulatory elements. Site-directed deletions of multiple transcription factors binding sites (TFBS), including Yin Yang-1(YY1), TATA-binding protein (TBP), sex-determining region Y-box2 (SOX2), and cyclin-dependent kinase 8 (CDK8) binding sites, markedly inhibited the ORF3 promoter activity. Moreover, overexpression of these transcription factors in CCB cells also led to a noticeable reduction in ORF3 promoter activity. Importantly, YY1, TBP, SOX2, and CDK8 played antiviral roles against CyHV-3 infection, as evidenced by decreased viral transcripts (ORF55, ORF81, and ORF92) and genome copies after overexpression of these TFs followed by CyHV-3 infection. Collectively, CyHV-3 replication was markedly inhibited by reducing the promoter activity of ORF3 mediated by multiple cellular TFs. These findings enhance our understanding of the role of IE gene promoters in CyHV-3 and lays a foundation for in-depth studies on viral gene transcriptional regulation mechanisms.

A novel deep learning identifier for promoters and their strength using heterogeneous features

Promoters, which are short (50–1500 base-pair) in DNA regions, have emerged to play a critical role in the regulation of gene transcription. Numerous dangerous diseases, likewise cancer, cardiovascular, and inflammatory bowel diseases, are caused by genetic variations in promoters. Consequently, the correct identification and characterization of promoters are significant for the discovery of drugs. However, experimental approaches to recognizing promoters and their strengths are challenging in terms of cost, time, and resources. Therefore, computational techniques are highly desirable for the correct characterization of promoters from unannotated genomic data. Here, we designed a powerful bi-layer deep-learning based predictor named “PROCABLES“, which discriminates DNA samples as promoters in the first-phase and strong or weak promoters in the second-phase respectively. The proposed method utilizes five distinct features, such as word2vec, k-spaced nucleotide pairs, trinucleotide propensity-based features, trinucleotide composition, and electron–ion interaction pseudopotentials, to extract the hidden patterns from the DNA sequence. Afterwards, a stacked framework is formed by integrating a convolutional neural network (CNN) with bidirectional long-short-term memory (LSTM) using multi-view attributes to train the proposed model. The PROCABLES model achieved an accuracy of 0.971 and 0.920 and the MCC 0.940 and 0.840 for the first and second-layer using the ten-fold cross-validation test, respectively. The predicted results anticipate that the proposed PROCABLES protocol outperformed the advanced computational predictors targeting promoters and their types. In summary, this research will provide useful hints for the recognition of large-scale promoters in particular and other DNA problems in general.

Repetitive Sequence Stability in Embryonic Stem Cells.

Repetitive sequences play an indispensable role in gene expression, transcriptional regulation, and chromosome arrangements through trans and cis regulation. In this review, focusing on recent advances, we summarize the epigenetic regulatory mechanisms of repetitive sequences in embryonic stem cells. We aim to bridge the knowledge gap by discussing DNA damage repair pathway choices on repetitive sequences and summarizing the significance of chromatin organization on repetitive sequences in response to DNA damage. By consolidating these insights, we underscore the critical relationship between the stability of repetitive sequences and early embryonic development, seeking to provide a deeper understanding of repetitive sequence stability and setting the stage for further research and potential therapeutic strategies in developmental biology and regenerative medicine.

Omega-3 Fatty Acids and Arrhythmias.

The pro- and antiarrhythmic effects of omega-3 polyunsaturated fatty acids (n-3 PUFAs) have been extensively studied in preclinical and human trials. Despite early evidence of an antiarrhythmic role of n-3 PUFA in the prevention of sudden cardiac death and postoperative and persistent atrial fibrillation (AF), subsequent well-designed randomized trials have largely not shown an antiarrhythmic benefit. Two trials that tested moderate and high-dose n-3 PUFA demonstrated a reduction in sudden cardiac death, but these findings have not been widely replicated, and the potential of eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA) to reduce arrhythmic death in combination, or as monotherapy, remains uncertain. The accumulated clinical evidence does not support supplementation of n-3 PUFA for postoperative AF or secondary prevention of AF. Several large, contemporary, randomized controlled trials of high-dose n-3 PUFA for primary or secondary cardiovascular prevention have demonstrated a small, significant, dose-dependent increased risk of incident AF compared with mineral oil or corn oil comparator. These findings were reproduced with both icosapent ethyl monotherapy and a mixed EPA+DHA formulation. The proarrhythmic mechanism of increased AF in contemporary cohorts exposed to high-dose n-3 PUFA is unknown. EPA and DHA and their metabolites have pleiotropic cardiometabolic and pro- and antiarrhythmic effects, including modification of the lipid raft microenvironment; alteration of cell membrane structure and fluidity; modulation of sodium, potassium, and calcium currents; and regulation of gene transcription, cell proliferation, and inflammation. Further characterization of the complex association between EPA, EPA+DHA, and DHA and AF is needed. Which formulations, dose ranges, and patient subgroups are at highest risk, remain unclear.

Design and construction of light-regulated gene transcription and protein translation systems in yeast P. Pastoris

IntroductionP. pastoris is a common host for effective biosynthesis of heterologous proteins as well as small molecules. Accurate regulation of gene transcription and protein synthesis is necessary to coordinate synthetic gene circuits and optimize cellular energy distribution. Traditional methanol or other inducible promoters, natural or engineered, have defects in either fermentation safety or expression capacity. The utilization of chemical inducers typically adds complexity to the product purification process, but there is no other well-controlled protein synthesis system than promoters yet. ObjectiveThe study aimed to address the aforementioned challenges by constructing light-regulated gene transcription and protein translation systems with excellent expression capacity and light sensitivity. MethodsTrans-acting factors were designed by linking the N. crassa blue-light sensor WC-1 with the activation domain of endogenous transcription factors. Light inducible or repressive promoters were then constructed through chimeric design of cis-elements (light-responsive elements, LREs) and endogenous promoters. Various configurations of trans-acting factor/LRE pairs, along with different LRE positions and copy numbers were tested for optimal promoter performance. In addition to transcription, a light-repressive translation system was constructed through the “rare codon brake” design. Rare codons were deliberately utilized to serve as brakes during protein synthesis, which were switched on and off through the light-regulated changes in the expression of the corresponding pLRE-tRNA. ResultsAs demonstrated with GFP, the light-inducible promoter 4pLRE-cPAOX1 was 70 % stronger than the constitutive promoter PGAP, with L/D ratio = 77. The light-repressive promoter PGAP-pLRE was strictly suppressed by light, with expression capacity comparable with PGAP in darkness. As for the light-repressive translation system, the “triple brake” design successfully eliminated leakage and achieved light repression on protein synthesis without any impact on mRNA expression. ConclusionThe newly designed light-regulated transcription and translation systems offer innovative tools that optimize the application of P. pastoris in biotechnology and synthetic biology.

Mitochondrial diabetes in mice expressing a dominant-negative allele of nuclear respiratory factor-1 (Nrf1) in pancreatic β-cells

Genetic polymorphisms in nuclear respiratory factor-1 (Nrf1), a key transcriptional regulator of nuclear-encoded mitochondrial proteins, have been linked to diabetes. Homozygous deletion of Nrf1 is embryonic lethal in mice. Our goal was to generate mice with β-cell-specific reduction in NRF1 function to investigate the relationship between NRF1 and diabetes. We report the generation of mice expressing a dominant-negative allele of Nrf1 (DNNRF1) in pancreatic β-cells. Heterozygous transgenic mice had high fed blood glucose levels detected at 3 wks of age, which persisted through adulthood. Plasma insulin levels in DNNRF1 transgenic mice were reduced, while insulin sensitivity remained intact in young animals. Islet size was reduced with increased numbers of apoptotic cells, and insulin content in islets by immunohistochemistry was low. Glucose-stimulated insulin secretion in isolated islets was reduced in DNNRF1-mice, but partially rescued by KCl, suggesting that decreased mitochondrial function contributed to the insulin secretory defect. Electron micrographs demonstrated abnormal mitochondrial morphology in β-cells. Expression of NRF1 target genes Tfam, Tfb1m and Tfb2m, and islet cytochrome c oxidase and succinate dehydrogenase activities were reduced in DNNRF1-mice. Rescue of mitochondrial function with low level activation of transgenic c-Myc in β-cells was sufficient to restore β-cell mass and prevent diabetes. This study demonstrates that reduced NRF1 function can lead to loss of β-cell function and establishes a model to study the interplay between regulators of bi-genomic gene transcription in diabetes.

P300 regulates histone crotonylation and preimplantation embryo development

Histone lysine crotonylation, an evolutionarily conserved modification differing from acetylation, exerts pivotal control over diverse biological processes. Among these are gene transcriptional regulation, spermatogenesis, and cell cycle processes. However, the dynamic changes and functions of histone crotonylation in preimplantation embryonic development in mammals remain unclear. Here, we show that the transcription coactivator P300 functions as a writer of histone crotonylation during embryonic development. Depletion of P300 results in significant developmental defects and dysregulation of the transcriptome of embryos. Importantly, we demonstrate that P300 catalyzes the crotonylation of histone, directly stimulating transcription and regulating gene expression, thereby ensuring successful progression of embryo development up to the blastocyst stage. Moreover, the modification of histone H3 lysine 18 crotonylation (H3K18cr) is primarily localized to active promoter regions. This modification serves as a distinctive epigenetic indicator of crucial transcriptional regulators, facilitating the activation of gene transcription. Together, our results propose a model wherein P300-mediated histone crotonylation plays a crucial role in regulating the fate of embryonic development.

The Effects of trans-10, cis-12 Conjugated Linoleic Acid on the Production Performance of Dairy Cows and the Expression and Transcription Regulation of Lipid Metabolism-Related Genes in Bovine Mammary Epithelial Cells.

Dietary fatty acids (FAs) determine the quality of dairy products. The trans-10, cis-12 conjugated linoleic acid (t10c12-CLA) is commonly considered an FA factor leading to milk fat depression syndrome (MFDs) in dairy cow. However, its effect on dairy cow performance and involvement in milk fat metabolism have been insufficiently explored. This study administered 136.17 g/day of rumen-protected CLA (RP-CLA) to dairy cows and found a diminution in milk fat percentage and a trend of increasing milk protein percentage on day 21 postpartum. Lactose content, milk yield, and net energy for lactation were unaffected. In the cell experiments, Oil Red O staining showed a notable increase in lipid droplets. Gene and protein expression analysis showed that 300 μM t10c12-CLA upregulated the expression of CD36, DGAT2, and ADRP, while downregulating the expression of ACACA, FASN, SREBP1, FABP3, FATP3, ACSL4, LPIN1, DGAT1, BTN1A1, XDH, SNAP23, and VAMP4. This provides a possible mechanistic pathway for the contradictory phenomenon of t10c12-CLA reducing milk fat while increasing lipid droplets. Overall, t10c12-CLA, as a long-chain fatty acid, can promote lipid droplet synthesis but may reduce milk fat by inhibiting lipid droplet fusion and secretion, FAs de novo synthesis, and triglyceride biosynthesis.

Roles of Lysine Methylation in Glucose and Lipid Metabolism: Functions, Regulatory Mechanisms, and Therapeutic Implications.

Glucose and lipid metabolism are essential energy sources for the body. Dysregulation in these metabolic pathways is a significant risk factor for numerous acute and chronic diseases, including type 2 diabetes (T2DM), Alzheimer's disease (AD), obesity, and cancer. Post-translational modifications (PTMs), which regulate protein structure, localization, function, and activity, play a crucial role in managing cellular glucose and lipid metabolism. Among these PTMs, lysine methylation stands out as a key dynamic modification vital for the epigenetic regulation of gene transcription. Emerging evidence indicates that lysine methylation significantly impacts glucose and lipid metabolism by modifying key enzymes and proteins. This review summarizes the current understanding of lysine methylation's role and regulatory mechanisms in glucose and lipid metabolism. We highlight the involvement of methyltransferases (KMTs) and demethylases (KDMs) in generating abnormal methylation signals affecting these metabolic pathways. Additionally, we discuss the chemical biology and pharmacology of KMT and KDM inhibitors and targeted protein degraders, emphasizing their clinical implications for diseases such as diabetes, obesity, neurodegenerative disorders, and cancers. This review suggests that targeting lysine methylation in glucose and lipid metabolism could be an ideal therapeutic strategy for treating these diseases.

Effects of Sodium-Glucose Cotransporter 2 Inhibitors on Transcription Regulation of AgRP and POMC Genes.

Sodium-glucose cotransporter 2 (SGLT2) inhibitors regulate plasma glucose levels in patients with type 2 diabetes mellitus (T2DM) by inhibiting renal glucose reabsorption. This study investigated the impact of empagliflozin (EMPA), an SGLT2 inhibitor, on hypothalamic energy regulation. To directly investigate the role of SGLT2 inhibitors in the hypothalamus, we administered EMPA through intracerebroventricular (i.c.v.) injections into the murine ventricles. After dental cementing the i.c.v. cannula onto the skull, the mice were given 5 days to recover before receiving vehicle or EMPA (50 nM/2 μL) injections. In a high-fat diet (HFD)-induced obesity model, we determined the gene expression levels of agouti-related peptide (AgRP) and pro-opiomelanocortin (POMC) in the hypothalamus. Additionally, we assessed FoxO1 expression, which regulates AgRP and POMC gene transcription in hypothalamic cell lines. We found that EMPA directly influenced the expression of endogenous mRNA of POMC and AgRP, which are critical for energy homeostasis, and modulated their transcription in high-fat diet-induced obese mice. Additionally, EMPA affected the expression of FoxO1, a key transcriptional regulator of glucose homeostasis, thereby regulating the transcriptional activity of POMC and AgRP. These results indicate that EMPA significantly influences hypothalamic energy homeostasis, highlighting its potential as a regulator in obesity and T2DM management.

Unraveling the modulatory manner and function of circRNAs in the Asian honey bee larval guts.

Circular RNAs (circRNAs) are a class of non-coding RNAs (ncRNAs) that can participate in biological processes such as gene expression, growth, and development. However, little has been explored about the function of circRNAs in the development of Apis cerana larval guts. By using our previously gained deep sequencing data from the guts of A. cerana worker larvae at 4-, 5-, and 6-day-old (Ac4, Ac5, and Ac6 groups), the expression pattern and regulatory role of circular RNAs (circRNAs) during the development process was comprehensively investigated, with a focus on differentially expressed circRNAs (DEcircRNAs) relevant to immunity pathways and developmental signaling pathways, followed by validation of the binding relationships among a key competing endogenous RNA (ceRNA) axis. Here, 224 (158) DEcircRNAs were detected in the Ac4 vs. Ac5 (Ac5 vs. Ac6) comparison group. It's suggested that 172 (123) parental genes of DEcircRNAs were involved in 26 (20) GO terms such as developmental process and metabolic process and 138 (136) KEGG pathways like Hippo and Wnt signaling pathways. Additionally, ceRNA network analysis indicated that 21 (11) DEcircRNAs could target seven (three) DEmiRNAs, further targeting 324 (198) DEmRNAs. These DEmRNAs can be annotated to 33 (26) GO terms and 168 (200) KEGG pathways, including 12 (16) cellular and humoral immune pathways (endocytosis, lysosome, Jak-STAT, etc.) and 10 (nine) developmental signaling pathways (Hippo, mTOR, Hedgehog, etc.). Interestingly, DEcircRNAs in these two comparison groups could target the same ace-miR-6001-y, forming complex sub-networks. The results of PCR and Sanger sequencing confirmed the back-splicing sites within four randomly selected DEcircRNAs. RT-qPCR detection of these four DEcircRNAs verified the reliability of the used transcriptome data. The results of dual-luciferase reporter assay verified the binding relationships between novel_circ_001627 and ace-miR-6001-y and between ace-miR-6001-y and apterous-like. Our data demonstrated that DEcircRNAs were likely to modulate the developmental process of the A. cerana worker larval guts via regulation of parental gene transcription and ceRNA network, and novel_circ_001627/ace-miR-6001-y/apterous-like was a potential regulatory axis in the larval gut development. Findings from this work offer a basis and a candidate ceRNA axis for illustrating the circRNA-modulated mechanisms underlying the A. cerana larval guts.

VIK-Mediated Auxin Signaling Regulates Lateral Root Development in Arabidopsis.

The crucial role of TIR1-receptor-mediated gene transcription regulation in auxin signaling has long been established. In recent years, the significant role of protein phosphorylation modifications in auxin signal transduction has gradually emerged. To further elucidate the significant role of protein phosphorylation modifications in auxin signaling, a phosphoproteomic analysis in conjunction with auxin treatment has identified an auxin activated Mitogen-activated Protein Kinase Kinase Kinase (MAPKKK) VH1-INTERACTING Kinase (VIK), which plays an important role in auxin-induced lateral root (LR) development. In the vik mutant, auxin-induced LR development is significantly attenuated. Further investigations show that VIK interacts separately with the positive regulator of LR development, LATERAL ORGAN BOUNDARIES-DOMAIN18 (LBD18), and the negative regulator of LR emergence, Ethylene Responsive Factor 13 (ERF13). VIK directly phosphorylates and stabilizes the positive transcription factor LBD18 in LR formation. In the meantime, VIK directly phosphorylates the negative regulator ERF13 at Ser168 and Ser172 sites, causing its degradation and releasing the repression by ERF13 on LR emergence. In summary, VIK-mediated auxin signaling regulates LR development by enhancing the protein stability of LBD18 and inducing the degradation of ERF13, respectively.

IProL: identifying DNA promoters from sequence information based on Longformer pre-trained model

Promoters are essential elements of DNA sequence, usually located in the immediate region of the gene transcription start sites, and play a critical role in the regulation of gene transcription. Its importance in molecular biology and genetics has attracted the research interest of researchers, and it has become a consensus to seek a computational method to efficiently identify promoters. Still, existing methods suffer from imbalanced recognition capabilities for positive and negative samples, and their recognition effect can still be further improved. We conducted research on E. coli promoters and proposed a more advanced prediction model, iProL, based on the Longformer pre-trained model in the field of natural language processing. iProL does not rely on prior biological knowledge but simply uses promoter DNA sequences as plain text to identify promoters. It also combines one-dimensional convolutional neural networks and bidirectional long short-term memory to extract both local and global features. Experimental results show that iProL has a more balanced and superior performance than currently published methods. Additionally, we constructed a novel independent test set following the previous specification and compared iProL with three existing methods on this independent test set.