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Abiotic stresses, predominately drought, heat, salinity, cold, and waterlogging, adversely affect cereal crops. They limit barley production worldwide and cause huge economic losses. In barley, functional genes under various stresses have been identified over the years and genetic improvement to stress tolerance has taken a new turn with the introduction of modern gene-editing platforms. In particular, clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 (Cas9) is a robust and versatile tool for precise mutation creation and trait improvement. In this review, we highlight the stress-affected regions and the corresponding economic losses among the main barley producers. We collate about 150 key genes associated with stress tolerance and combine them into a single physical map for potential breeding practices. We also overview the applications of precise base editing, prime editing, and multiplexing technologies for targeted trait modification, and discuss current challenges including high-throughput mutant genotyping and genotype dependency in genetic transformation to promote commercial breeding. The listed genes counteract key stresses such as drought, salinity, and nutrient deficiency, and the potential application of the respective gene-editing technologies will provide insight into barley improvement for climate resilience.
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CCAAT enhancer binding protein β (C/EBPβ), as a nuclear transcription factor necessary for the development of liver, airway epithelium, and adipose tissue, plays a vital role in physiological processes related to cell proliferation, apoptosis, and differentiation. However, the up-regulation of C/EBPβ activates signal pathways related to inflammatory response, epithelial-mesenchymal transition, cell proliferation and invasion, immune response, and angiogenesis by regulating a series of downstream genes transcription promotes the development of lung diseases. Therefore, targeting C/EBPβ may be a potential treatment strategy for lung diseases. This paper summarizes the regulatory effects of C/EBPβ and related signaling pathways in lung infection, asthma, chronic obstructive pulmonary disease, lung injury, pulmonary fibrosis, and lung cancer to provide a theoretical basis for the precision medicine of lung diseases.
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It is known that hepatitis B virus (HBV) covalently closed circular DNA (cccDNA) persists in the nucleus of infected hepatocytes in the form of minichromosome and is difficult to target and eliminate. Studies on the mechanisms and strategies for persistent silencing or elimination of HBV cccDNA are the focus achieving for “functional cure” of chronic hepatitis B. This article introduces the current knowledge on the basic biological features of cccDNA, regulatory mechanisms of transcription and metabolism, and related host factors, with a focus on the potential pathways and strategies for cccDNA silencing or elimination.
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Unraveling the genetic basis of medicinal plant metabolism and developmental traits is a long-standing goal for pharmacologists and plant biologists. This paper discusses the definition of molecular genetics of medicinal plants, which is an integrative discipline with medicinal plants as the research object. This discipline focuses on the heredity and variation of medicinal plants, and elucidates the relationship between the key traits of medicinal plants(active compounds, yield, resistance, etc.) and genotype, studies the structure and function, heredity and variation of medicinal plant genes mainly at molecular level, so as to reveal the molecular mechanisms of transmission, expression and regulation of genetic information of medicinal plants. Specifically, we emphasize on three major aspects of this discipline.(1)Individual and population genetics of medicinal plants, this part mainly highlights the genetic mechanism of the domestication, the individual genomics at the species level, and the formation of genetic diversity of medicinal plants.(2)Elucidation of biosynthetic pathways of active compounds and their evolutionary significance. This part summarizes the biosynthesis, diversity and molecular evolution of active compounds in medicinal plants.(3) Molecular mechanisms that shaping the key agronomic traits by internal and external factors. This part focuses on the accumulation and distribution of active compounds within plants and the regulation of metabolic network by environmental factors. Finally, we prospect the future direction of molecular genetics of medicinal plants based on the rapid development of multi-omics technology, as well as the application of molecular genetics in the future strategies to achieve conservation and breeding of medicinal plants and efficient biosynthesis of active compounds.
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Biosynthetic Pathways , Genomics , Molecular Biology , Plant Breeding , Plants, MedicinalABSTRACT
OBJECTIVE To functionally analyze the promoter using dual luciferases reporter assay system by cloning the promoter region of mouse interferon-y receptor 2 (Ifngr2) gene. METHODS The 5' sequence (-1344-+48) containing the transcription start site of the mouse Ifngr2 gene was acquired from the Eukaryotic Promoter Database, and the gene fragment was cloned into the luciferase reporter vector. Series of 5' deleted truncated variants were further constructed to obtain six luciferase reporter vectors with different lengths of promoters. The transcriptional activity of different Ifngr2 promoter truncations was determined by the dual luciferase analysis. In addition, site-directed mutation was applied to explore the effect of NF-kB on mouse Ifngr2 transcription. RESULTS The constructed mouse Ifngr2 promoter luciferase reporter vector was confirmed by gene sequencing and alignment. Promoter deletion analysis showed that the-132-97 and-1059-727 regions were important for mouse Ifngr2 gene transcription. Site-directed mutation indicated that the NF-kB binding region was essential for the transcription of Ifngr2 gene. CONCLUSION Mouse Ifngr2 gene promoter luciferase vectors are successfully constructed. Functional analysis of the mouse Ifngr2 gene promoter reveals an NF-kB binding site, which is essential for transcription of Ifngr2 gene.
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MarR family transcription regulators are ubiquitous among bacteria and archaea. They extensively control multiple cellular processes and elaborately regulate the expression of genes involved in virulence, stress response and antibiotics at translational level. In Xanthomonas campestris pv. campestris, insertional inactivation of MarR family transcription regulator HpaR (XC2827) resulted in significantly decrease in virulence and increase in the production of the extracellular proteases. Here, we reported that the genome of Xcc 8004 encodes nine MarR family transcription regulators. The MarR family transcription regulators, HpaR (XC2827) and XC0449, were heterologous expressed and purified. In vitro MST and Pull-down assay confirmed the physical interaction between HpaR and XC0449. Phenotypical assay determined that deletion of XC0449 resulted in substantial virulence attenuation. In vitro EMSA, in vivo qRT-PCR and GUS activity assay identified that HpaR and XC0449 coordinately act as the transcriptional activator to regulate the expression of the virulence-associated gene XC0705, and eventually control the bacterial virulence and the production of extracellular proteases.
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Bacterial Proteins , Gene Expression Regulation, Bacterial , Transcription Factors , Virulence , Xanthomonas campestrisABSTRACT
Mitochondrial dysfunctions play major roles in ageing. How mitochondrial stresses invoke downstream responses and how specificity of the signaling is achieved, however, remains unclear. We have previously discovered that the RNA component of Telomerase TERC is imported into mitochondria, processed to a shorter form TERC-53, and then exported back to the cytosol. Cytosolic TERC-53 levels respond to mitochondrial functions, but have no direct effect on these functions, suggesting that cytosolic TERC-53 functions downstream of mitochondria as a signal of mitochondrial functions. Here, we show that cytosolic TERC-53 plays a regulatory role on cellular senescence and is involved in cognition decline in 10 months old mice, independent of its telomerase function. Manipulation of cytosolic TERC-53 levels affects cellular senescence and cognition decline in 10 months old mouse hippocampi without affecting telomerase activity, and most importantly, affects cellular senescence in terc cells. These findings uncover a senescence-related regulatory pathway with a non-coding RNA as the signal in mammals.
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In mammalian cells, transcribed enhancers (TrEns) play important roles in the initiation of gene expression and maintenance of gene expression levels in a spatiotemporal manner. One of the most challenging questions is how the genomic characteristics of enhancers relate to enhancer activities. To date, only a limited number of enhancer sequence characteristics have been investigated, leaving space for exploring the enhancers' DNA code in a more systematic way. To address this problem, we developed a novel computational framework, Transcribed Enhancer Landscape Search (TELS), aimed at identifying predictive cell type/tissue-specific motif signatures of TrEns. As a case study, we used TELS to compile a comprehensive catalog of motif signatures for all known TrEns identified by the FANTOM5 consortium across 112 human primary cells and tissues. Our results confirm that combinations of different short motifs characterize in an optimized manner cell type/tissue-specific TrEns. Our study is the first to report combinations of motifs that maximize classification performance of TrEns exclusively transcribed in one cell type/tissue from TrEns exclusively transcribed in different cell types/tissues. Moreover, we also report 31 motif signatures predictive of enhancers' broad activity. TELS codes and material are publicly available at http://www.cbrc.kaust.edu.sa/TELS.
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Humans , Enhancer Elements, Genetic , Genomics , Methods , Nucleotide Motifs , Sequence Analysis, DNA , Methods , Transcription, GeneticABSTRACT
Transcriptional regulation is crucial for regulated gene expression. Due to the complexity, it has been difficult to engineer eukaryotic transcription factor (TF) and promoter pairs. The few availabilities of eukaryotic TF and promotor pairs limit their practical use for clinical or industrial applications. Here, we report a de novo construction of synthetic inhibitory transcription factor and promoter pairs for mammalian transcriptional regulation. The design of synthetic TF was based on the fusion of DNA binding domain and Kruppel associated box transcription regulating domain (KRAB). The synthetic promoter was constructed by inserting the corresponding TF response element after SV40 promoter. We constructed and tested five synthetic inhibitory transcription factor and promoter pairs in cultured mammalian cells. The inhibition capability and orthogonality were verified by flow cytometry. In summary, we demonstrate the feasibility of constructing mammalian inhibitory TF and promoter pairs, which could be standardized for advanced gene-circuit design and various applications in the mammalian synthetic biology.
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Animals , Gene Expression Regulation , Gene Regulatory Networks , Mammals , Promoter Regions, Genetic , Transcription Factors , Transcription, GeneticABSTRACT
Circular RNAs(circRNAs)are a type of covalently closed circular non-coding RNAs that are ex-pressed across varieties of life forms.CircRNAs have a variety of characteristics such as stable structures, tissue-specific expression and the function of microRNA sponges in the regulation of genes.CircRNAs are abundant,highly expressed in neural tissues,emerging evidence also indicates that circRNAs play an important role in the pathophysiologic process of Alzheimer's disease, Parkinson's disease, amyotrophic lateral sclerosis and other neurological diseases.As one of the most important neurological diseases,the pathogenesis of brain damage and repair after ischemia has not yet been evalua -ted,and stroke related circRNAs are of great significance.In this review,we summarize related regulations,and the poten-tial regulatory mechanisms of cicrcRNAs in cerebrovascular diseases, and the important role of circRNAs in post stroke pathophysiologic process is also discussed.CircRNAs are expected to be a new drug target,and provide new theoretical ba-sis for the diagnosis and treatment of cerebrovascular diseases.
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The bromodomains and extra-terminal domain (BET) family proteins recognize acetylated chromatin through their bromodomains (BDs) and help in regulating gene expression. BDs are chromatin ‘readers’: by interacting with acetylated lysines on the histone tails, they recruit chromatin-regulating proteins on the promoter region to regulate gene expression and repression. Extensive efforts have been employed by scientific communities worldwide to identify and develop potential inhibitors of BET family BDs to regulate protein expression by inhibiting acetylated histone (H3/H4) interactions. Several small molecule inhibitors have been reported, which not only have high affinity but also have high specificity to BET BDs. These developments make BET family proteins an important therapeutic targets for major diseases such as cancer, neurological disorders, obesity and inflammation. Here, we review and discuss the structural biology of BET family BDs and their applications in major diseases.
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Schistosomiasis is a kind of zoonosis with serious hazard,which is popular in many countries and regions in the world. One of the efforts for schistosomiasis prevent and control is developing new drugs and vaccines,and knowing the tran?scription regulation mechanism and the function of transcription factors will help us find the targets of new drugs and vaccines as soon as possible. This article reviews the progress of Schistosoma transcription factors and research methods.
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microRNAs ( miRNAs) are a family of short non-cod-ing RNAs that regulate the expression of target genes by binding to complementary regions. The miRNAs expression is readily al-tered by drugs, carcinogens, hormones, stress or diseases, and that might lead to changes in the drug metabolism, pharmacoki-netics or potency. Moreover, the evaluation of drug metabolic enzyme-related miRNAs would provide useful information for per-sonalized medicine. This review describes the current knowledge on the post-transcription regulation of drug metabolic enzymes by miRNAs.
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PURPOSE: Mitofusin2 gene (Mfn2, also named Hyperplasia suppressive gene, HSG) is very important in the origin and development of hypertension. However, the mechanism of Mfn2/HSG expression regulation was not uncovered. This study was designed to explore the association of a novel 5'-uncoding region (UCR) -1248 A>G variation of HSG/Mfn2 gene and hypertension. MATERIALS AND METHODS: 472 healthy, normotensive subjects [normotension (NT) group], 454 prehypertensive subjects [prehypertension (PH) group] and 978 hypertensive patients [essential hypertension (EH) group] were screened for an association study between 5'-UCR -1248 A>G of Mfn2/HSG and hypertension by polymerase chain reaction and DNA sequencing after venous blood was drawn and DNA was extracted. RESULTS: When comparing the A and G frequency in EH, PH and NT groups, in total, NT group significantly had higher A frequency than in PH group [odds ratio (OR)=1.605, confidence interval (CI) 95%=1.063-2.242, p=0.025] and EH group (OR=5.395, CI 95%=3.783-7.695, pG variation was significantly related with blood pressure level (B=-1.271, Wald=40.914, CI 95%=-1.660 - -0.881, pG variation of Mfn2/HSG gene was a novel variation and may be associated with hypertension in Chinese.
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Female , Humans , Male , China , GTP Phosphohydrolases/genetics , Gene Expression Regulation , Genetic Association Studies , Genotype , Hypertension/genetics , Logistic Models , Mitochondrial Proteins/genetics , Polymorphism, Single Nucleotide , Sequence Analysis, DNAABSTRACT
The protein HTRP (human transcription regulator protein) is encoded by the differential gene htrp and induced by Herpes simplex virus type 1 (HSV-1) infection in KMB-17 cells. HTRP was found to interact with SAP30 (mSin3A Association Protein), one of the components of co-repressor complex mSin3A, which is part of the deacetylation transfer enzyme HDAC. To reveal the biological significance of the interaction between HTRP and SAP30, real- time PCR and a dual-luciferase detecting system was used. The results indicate that HTRP could inhibit the transcription of a viral promoter, whose interaction with SAP30 synergistically affects transcriptional inhibition of the viral genes, and is related to HDAC enzyme activity. ChIP experiments demonstrate that HTRP could promote HDAC activity by increasing the deacetylation level of lysine 14 and lysine 9 in histone H3.
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High level of eetopie serum ACTH can not be suppressed by endogenous or exogenous glucocorticoid, this is the cardinal characteristic of ectopic ACTH syndrome (EAS), that is to say there exists glucocorticoid resistance in EAS. However, the mechanism of glucocorticoid resistance remains unclear. Identifying the mechanism can help us to diagnose and treat the disease. This review focuses on the mechanism of glucocorticoid resistance from several aspects, including the pre-glucocorticoid receptor (GR), GR and post-GR.
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Objective To investigate the relationship between PrfA-dependent promoters and PrfA regulation. Methods LacZ reporter gene fusions used to investigate the inhibitory elements for PrfA-dependent transcription were carried on two promoters of Listeria monocytogenes: a PrfA-dependent promoter of the phospholipase gene pica (PplcA) and a putative promoter of the aroA gene (ParoA2) which contains a similar PrfA-binding site (PrfA-box) and a similar-10 box as PplcA but does not function as PrfA-dependent promoter. A series of hybrid plcA-aroA promoters by exchanging corresponding sequence elements of these two "promoters" were constructed and incorporated into upstream of a promoterless lacZ gene. The variant promoter-lacZ transcriptional fusions were then electroporated into L. monocytogenes wild-type strain P14, prfA mutant P14a and prfA deletion mutant A42, respectively. The expression level of PrfA is the highest in the P14a and the lowest in A42. The corresponding transcription activities of hybrid promoters were measured by the β-galactosidase assay. Results The two critical elements of PrfA-dependent promoters, the PrfA-box and the-10 box, can be functionally exchanged as long as the distance in between is maintained 22 or 23 bp. However, the interspace sequence and the sequence downstream of the -10 box of ParoA2 were strongly inhibitory for PrfA-dependent transcription. Conclusion Downstream sequence together -10 box of ParoA2 might fold into a hairpin structure when present in a single stranded DNA and possibly block the formation of the transcriptional initiation open complex, hence, inhibit the PrfA-dependent transcription from ParoA2.
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Angiotensin Ⅱ(AngⅡ)can induce the expression of its precursor,angiotensinogen,in vascular smooth muscle cells(VSMC),which is related with increased activating protein-1(AP-1)binding to its cis-element located in the angiotensinogen gene promoter.In the present study,cycloheximide(CHX)was used as an inhibitor to interrupt c-Jun,the role of AP-1 in AngⅡ-induced its precursor gene activation was investigated by DNA-protein interaction and immunoblotting.The results showed that the level of c-Jun,the component of transcription factor AP-1,was significantly increased in the nucleus of VSMC after AngⅡ treatment.The majority of c-Jun was found in the nucleus but hardly detected in the cytoplasm by immunocytochemistry staining.Immunoprecipitation assays confirmed that AngⅡ could induce serine phosphorylation of c-Jun.EMSA results indicated that the level of phosphorylated of c-Jun had a positive correlation with AP-1 binding activity to cis-acting element of angiotensinogen gene and transcription activation of angiotensinogen.CHX inhibited AngⅡ-induced binding activity of AP-1 by reducing the phosphorylation of c-Jun,though it did not affect the expression of c-Jun.These findings suggest that the AP-1 phosphorylation induced by AngⅡ is one of the important mechanisms whereby AngⅡ regulates its precursor gene expression in feedback manner.It is found that CHX is an inhibitor to phosphorylation of c-Jun.
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Eukaryotic DNA element called Matrix Attachment Regions (MARs) can function on regulating the structure and activity of chromosome. Traditional quantitation in vitro and indirect functional analysis can not always reflect MAR-involved physiological state. In order to study transcription regulation and make a try in methodism,? 1-antitrypsin MAR (?1-AT MAR) is cloned and incorporated into pEGFP-C1 vector. Non-MAR-containing and MAR-containing plasmids were then transfected into HEK-293 cells with LipofectamineTM 2000 respectively. Positive cell clones were assayed after 20 days of selection by G418. Semiquantitative RT-PCR and fluorescence microscope analysis show that this MAR has a positive effect on modulating nearby gene expression. Further, co-localization with newly CMV promoter and RNA polymeraseⅡ(RNAPⅡ) was detected by chromatin immunoprecipitation (ChIP), The PCR result demonstrates that more RNAPⅡwas recruited to the CMV promoter to initiate transcription in presence of MAR. ChIP can be used to confirm the MAR-mediated transcriptional activation and provide more reliable information than RT-PCR in real time. The technology is also providing a platform for our research in gene expression regulation.
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; 3. therapy with A&A (A&A); 4. Astragali alone (A); 5. Astragali polysac-charide Ⅰ (APⅠ); 6. AP Ⅱ ; 7. Astragali glucoside (AG), Results The level of serum albumin,albumin mRNA and albumin gene transcription were measured by biochemistry, Northern blot hybridization, nuclear run-on assay and quantity in laser density screening. The level of serum albumin in N was significantly lower than C. The serum albumin concentration in each therapy group was higher than N group. The transcription of the albumin gene was higher in N than in C and highest in A&A. The alterations of northern blot hybridization were same as the transcription results. But both the level of albumin mRNA and the transcription of albumin gene in A, AP I , AP I and AG were no change compared with N. Conclusion A&A increases albumin mRNA expression at least in part by improving the rate of gene transcription, which participate the protection of the decrease of serum albumin in NS. But the effect of A, AP 1 , AP I and AG may mediated by other unknown mechanisms.