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Nore, Beston F., Tayfoor Jalil Mahmoud, and Ban Mousa Rashid. "Sequence Verifications and Promoter Analysis of The Prolactin Gene." Journal of Zankoy Sulaimani - Part A 15, no. 1 (December 17, 2012): 71–77. http://dx.doi.org/10.17656/jzs.10234.
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Chiang, Jeffrey, Wai Lim Ku, Kairong Cui, Keji Zhao, and Richard J. Hodes. "The use of alternative promoters in T cell development." Journal of Immunology 200, no. 1_Supplement (May 1, 2018): 165.20. http://dx.doi.org/10.4049/jimmunol.200.supp.165.20.
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Abstract Many mammalian genes, including a number involved in immune development and function, use multiple promoters encoding expression of the same protein product. To understand the function of alternative promotors during T cell development, we carried out genome-wide RNA-Seq analysis of DN, DP, CD4 and CD8 thymocytes. 26% (2469/9595) of genes expressed by thymocytes used two or more alternative promotors at some point in T cell development. However, only 3.2% (80/2469) of the genes which utilized two or more promoters showed the difference of promotor activity among different T cell developmental stages which were validated by selected representative genes with qPCR assay. To analyze mechanisms of alternative promoter regulation, DNase hypersensitivity sites were mapped, and ChIP-Seq with anti-H3K4me3 antibodies was performed in the same thymic subpopulations. To determine the in vivo functional role of alternative promotors for T cell development, several genes were selected for study by deletion of individual promoters by CRISPR technology. We have initially generated mice with deletion of distal or proximal promotor of the lck gene and demonstrated distinct functional roles of the two promoters: the proximal lck promoter is critical for early stages of thymic T cell development while the distal promoter was necessary for normal T cell activation. Ongoing studies will characterize more broadly the functional role of alternative promoter expression in thymocyte development, and the mechanisms mediating selective promoter activity.
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He, Yang, Tao Zhao, Fang Chen, Changchun Song, Chongchao Zhong, and Zhi Luo. "Functional Analysis of the Promoter Regions of Two Apoptosis-Related Genes (Bcl-2 and Cycs) and Their Regulation by Zn in Yellow Catfish." International Journal of Molecular Sciences 22, no. 12 (June 11, 2021): 6291. http://dx.doi.org/10.3390/ijms22126291.
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B-cell lymphoma 2 (Bcl-2) and cytochrome c (Cycs) are two important proteins relevant to cellular apoptosis. In this study, we characterized the functions of the promoter regions of two apoptosis-related genes, Bcl-2 and Cycs, in yellow catfish Pelteobagrus fulvidraco. We obtained a 1989 bp Bcl-2 promoter and an 1830 bp Cycs promoter and predicted several key transcription factor binding sites (TFBSs) on the promoters, such as Kruppel-like factor 4 (KLF4), signal transducer and activator of transcription factor 3 (STAT3), forkhead box O (FOXO), metal-responsive element (MRE) and hepatocyte nuclear factor 1α (HNF-1α). Zinc (Zn) increased the activities of the Bcl-2 promoter but decreased the activities of the Cycs promoter. Metal-responsive transcription factor 1 (MTF-1) and HNF-1α directly bound with Bcl-2 and Cycs promoters, and they positively regulated the activity of the Bcl-2 promoter but negatively regulated the activity of the Cycs promoter. Zn promoted the binding ability of HNF-1α to the Bcl-2 promoter but decreased its binding ability to the Cycs promoter. However, Zn had no significant effect on the binding capability of MTF-1 to the regions of Bcl-2 and Cycs promoters. Zn upregulated the mRNA and total protein expression of Bcl-2 but downregulated the mRNA and total protein expression of Cycs. At the same time, Annexin V–FITC/PI staining showed that Zn significantly reduced the apoptosis of primary hepatocytes. For the first time, our study provides evidence for the MRE and HNF-1α response elements on the Bcl-2 and Cycs promoters, offering new insight into the mechanism by which Zn affects apoptosis in vertebrates.
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Zhu, Guangwei, Qiang Huang, Wei Zheng, Yongjian Huang, Jin Hua, Shugang Yang, Jinfu Zhuang, et al. "LPS Upregulated VEGFR-3 Expression Promote Migration and Invasion in Colorectal Cancer via a Mechanism of Increased NF-κB Binding to the Promoter of VEGFR-3." Cellular Physiology and Biochemistry 39, no. 5 (2016): 1665–78. http://dx.doi.org/10.1159/000447868.
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Background and Aim: Lipopolysaccharide(LPS) could promote the progression of colorectal cancer, but the specific regulatory mechanisms are largely unknown. So, this study aim to clarify the mechanisms that LPS upregulated VEGFR-3, which promotes colorectal cancer cells migration and invasion with a mechanism of increased NF-κB bind to the promoter of VEGFR-3. Methods: The present study examined the VEGFR-3 expression in colorectal cancer tissues and analyzed the relationship between the VEGFR-3 expression with clinical parameters. PCR, Western blot, CCK-8, colone formation assay, and Transwell assay detected that LPS promoted the migration and invasion and the role of VEGFR-3 in the process of colorectal carcinoma in vitro. Used the methods of promoter analysis, EMSA assay and ChIP assay to explore the mechanisms LPS increased the expression of VEGFR-3. Results: VEGFR-3 was significantly high expression in the colorectal cancer tissues. And the high expression was associated with the TNM stage and lymph node metastasis of colorectal cancer. LPS could promote the migration and invasion, which could be blocked by the neutralizing antibody IgG of VEGFR-3. And found that -159 nt to +65 nt was the crucial region of VEGFR-3 promoter. And detected that the NF-κB was important transcription factor for the VEGFR-3 promoter. And LPS could increase NF-κB binding to VEGFR-3 promoter and upregulated the expression of VEGFR-3 to exert biological functions. Conclusion: We have elucidated the relationship between LPS and the VEGFR-3 expression and revealed that VEGFR-3 play very important role in the process of LPS promoting the migration and invasion of colorectal cancer cells. Further illuminated the mechanism that LPS upregulated VEGFR-3 expression via increased NF-κB bind to the promoter of VEGFR-3.
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Arsenijevic, Slavica, and Ljubisa Topisirovic. "Molecular analysis of mutatedLactobacillus acidophiluspromoter-like sequence P15." Canadian Journal of Microbiology 46, no. 10 (October 1, 2000): 938–45. http://dx.doi.org/10.1139/w00-077.
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The promoter-like sequence P15 that was previously cloned from the chromosome of Lactobacillus acidophilus ATCC 4356 is active in Lactobacillus reuteri, Lactobacillus plantarum, Lactobacillus acidophilus, and Escherichia coli, but not in Lactococcus lactis. N-methyl-N-nitroso-N-guanidine (MNNG) mutagenesis of P15 was used to select for a promoter active in L. lactis MG1363. Molecular analysis of the mutated promoter (designated P16) revealed a 90 bp deletion and a T[Formula: see text]A transversion. This deletion, in combination with the addition to the transversion, created a promoter with putative -35 and -10 hexamers identical to the consensus promoter sequence found in E. coli and Bacillus subtilis vegetative promoters. The activity of P16 was measured by its ability to promote chloramphenicol resistance in different bacteria when inserted in the promoter-probe plasmid pBV5030 (designated pLA16). The MIC of chloramphenicol in L. lactis, L. reuteri, L. plantarum, E. coli, and L. acidophilus harbouring pLA16 were 30, 170, 180, >500, and 3 µg/mL, respectively. This represents an increase in promoter activity compared to P15 in L. reuteri of 3-fold, in L. plantarum of 9-fold, and in E. coli of at least 2.5-fold, but a decrease in L. acidophilus of 7-fold.Key words: Lactobacillus acidophilus, promoter-like sequence, mutagenesis.
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Schneider, Klaus, and Christoph F. Beck. "Promoter-probe vectors for the analysis of divergently arranged promoters." Gene 42, no. 1 (January 1986): 37–48. http://dx.doi.org/10.1016/0378-1119(86)90148-4.
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Wang, Y. "Green tissue-specific analysis of a cloned rbcS promoter from Lemna gibba." Czech Journal of Genetics and Plant Breeding 50, No. 3 (September 12, 2014): 235–40. http://dx.doi.org/10.17221/200/2013-cjgpb.
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Many plant genetic engineering taskss require the spatial expression of genes which in turn depends upon the availability of specific promoters. The present paper analyses the green-tissue characteristics of a new L. gibba rbcS promoter driving the expression of the gus gene in transgenic tobacco. A 1491 bp rbcS (small subunit of ribulose bisphosphate carboxylase) promoter was isolated from Lemna gibba. The sequence analysis revealed that this promoter is different from the previously reported rbcS promoter and is named SSU5C. A 1438 bp fragment of the SSU5C promoter was fused with the gus gene and transgenic tobacco plants were generated. The analysis of T<sub>1</sub> tobacco p1438-gus revealed that GUS expression driven by the SSU5C promoter was detected in the green part of vegetative organs. The promoter deletion analysis confirmed a region from position –152 to –49 relative to the start of transcription containing boxes X, Y and Z, while a positive regulatory region conferred green tissue-specific expression. Further functional analysis of constructs of box-X, Y, Z, which was fused with the basal SSU5C promoter, confirmed that the boxes X, Y and Z represent the new minimized functional promoter, respectively, and are able to direct green tissue-specific expression. This promoter may be used for gene expression in a tissue-specific manner in plant molecular breeding.
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Kininis, Miltiadis, and W. Lee Kraus. "A Global View of Transcriptional Regulation by Nuclear Receptors: Gene Expression, Factor Localization, and DNA Sequence Analysis." Nuclear Receptor Signaling 6, no. 1 (January 2008): nrs.06005. http://dx.doi.org/10.1621/nrs.06005.
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Recent genomic analyses of transcription factor binding, histone modification, and gene expression have provided a global view of transcriptional regulation by nuclear receptors (NRs) that complements an existing large body of literature on gene-specific studies. The picture emerging from these genomic studies indicates that NRs bind at promoter-proximal and promoter-distal enhancers in conjunction with other transcription factors (e.g., activator protein-1, Sp1 and FOXA1). This binding promotes the recruitment of coregulators that mediate the posttranslational modification of histones at promoters and enhancers. Ultimately, signaling through liganded NRs stimulates changes in the occupancy of RNA polymerase II (Pol II) or the activation of preloaded Pol II at target promoters. Chromosomal looping and/or Pol II tracking may underlie promoter-enhancer communication. Interestingly, the direct target genes of NR signaling represent a limited subset of all the genes regulated by NR ligands, with the rest being regulated through secondary effects. As suggested by previous gene-specific analyses, NR-mediated outcomes are highly cell type- and promoter-specific, highlighting the complexity of transcriptional regulation by NRs and the value of genomic analyses for identifying commonly shared patterns. Overall, NRs share common themes in their patterns of localization and transcriptional regulation across mammalian genomes. In this review, we provide an overview of recent advances in the understanding of NR-mediated transcription garnered from genomic analyses of gene expression, factor localization, and target DNA sequences.
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Chen, Shu-Wei, Kun Wu, Wu-Hong Lv, Fang Chen, Chang-Chun Song, and Zhi Luo. "Functional Analysis of Two Zinc (Zn) Transporters (ZIP3 and ZIP8) Promoters and Their Distinct Response to MTF1 and RREB1 in the Regulation of Zn Metabolism." International Journal of Molecular Sciences 21, no. 17 (August 26, 2020): 6135. http://dx.doi.org/10.3390/ijms21176135.
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ZIP (zinc-regulated transporters, iron-regulated transporter-like protein) family plays an important role in organism Zn balance. This research identified the promoter regions of ZIP3 and ZIP8, two members of ZIP family, from a freshwater teleost yellow catfish Pelteobagrus fulvidraco, characterized the binding sequences of the metal-responsive transcription factor-1 (MTF-1) and Ras responsive element binding protein 1 (RREB1) on their promoter regions. The present study cloned and obtained the 2027 bp of ZIP3 promoter and 1664 bp of ZIP8 promoter, and predicted several key elements on their promoters, such as the binding sites of CREB (cAMP-response element binding protein), KLF4 (Kruppel like factor 4), MTF-1 and RREB1. The sequence deletion from −361 bp to −895 bp down-regulated the luciferase activity of ZIP3 promoter, and the deletion from −897 bp to −1664 bp down-regulated the luciferase activity of ZIP8 promoter. Within different deletion plasmids, the relative luciferase activities of ZIP3 and ZIP8 promoters changes to Zn incubation in a Zn concentration-dependent manner. The site mutagenesis and EMSA (electrophoretic mobility shift assay) found that the −1327 bp/−1343 bp MTF-1 binding site and the −248 bp/−267 bp RREB1 binding site on the ZIP3 promoter, and the −1543 bp/−1557 bp MTF-1 binding site on the ZIP8 promoter are functional sites. Low Zn increased the binding capability between MTF-1 and its responsive site on the ZIP3 promoter, and high Zn increased the transcriptional activation ZIP3 by RREB1; Zn also promoted the binding ability between MTF-1 and its responsive element on the ZIP8 promoter. This study provides the first direct evidence for the response elements of MTF-1 and RREB1 on ZIP3 and MTF-1 on ZIP8 to Zn, which are very important for the evaluation of Zn nutrition and toxicity in vertebrates.
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Choi, Jae Young, Soo-Jin Kwon, Jong Yul Roh, Tae-Jin Yang, Ming Shun Li, Beom-Seok Park, Yonggyun Kim, Soo-Dong Woo, Byung Rae Jin, and Yeon Ho Je. "Analysis of promoter activity of selected Cotesia plutellae bracovirus genes." Journal of General Virology 90, no. 5 (May 1, 2009): 1262–69. http://dx.doi.org/10.1099/vir.0.009472-0.
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In a previous study, we cloned 27 discrete genome segments of Cotesia plutellae bracovirus (CpBV) and provided the complete nucleotide sequences and annotation. Seven putative coding regions were predicted from one of the largest segments, CpBV-S30. The activity of promoters associated with six predicted ORFs from this segment were investigated using both transient and baculovirus expression assays with enhanced green fluorescent protein as a reporter gene. CpBV promoters showed activity earlier than the polyhedrin promoter and the activity of some of these promoters was superior to that of the Autographa californica multiple nucleopolyhedrovirus (AcMNPV) ie-1 promoter in the baculovirus expression assays. The promoter of ORF3004 showed the highest level of activity in insect cells, exhibiting 24 % of the activity obtained with the AcMNPV polyhedrin promoter in Sf9 cells. In Spodoptera exigua larvae, the ORF3006 promoter showed the highest activity, with about 35 % of the activity measured with the polyhedrin promoter. In addition, analysis of the ORF3006 promoter revealed that the region between −382 and −422 from the translation start point was critical for activity of this promoter. These results suggest that the CpBV-S30 promoters characterized here could be useful tools in a variety of biotechnological applications, such as gene expression analyses and insecticide development.
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O’Callaghan, Chris, Da Lin, and Thomas K. Hiron. "Intragenic transcriptional interference regulates the human immune ligand MICA." Journal of Immunology 200, no. 1_Supplement (May 1, 2018): 109.23. http://dx.doi.org/10.4049/jimmunol.200.supp.109.23.
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Abstract Regulation of MICA expression is incompletely understood, but human MICA can be upregulated in cancer cells, virus-infected cells and rapidly proliferating cells. Binding of MICA to the activating NKG2D receptor on cytotoxic immune cells promotes elimination of the cell expressing MICA. We noted that MICA has tandem promoters that drive overlapping forward transcription. We show that the MICA gene contains a conserved upstream promoter that expresses a non coding transcript. Transcription from the upstream promoter represses transcription from the standard downstream MICA promoter in cis through transcriptional interference. The effect of transcriptional interference depends on the strength of transcription from the upstream promoter and quantitative studies show that it is described by a simple reciprocal repressor function. The time course of transcriptional interference coincides with recruitment at the standard downstream promoter of factors involved in nucleosomal remodeling during transcription. Transcriptional interference is demonstrated in the regulation of MICA expression by the physiological inputs interferon-γ and interleukin-4, that both act through regulatory DNA elements in the upstream promoter. These findings have significant implications for the understanding of MICA expression. Transcription factors activating the downstream promoter will upregulate MICA expression, whereas transcription factors activating the upstream promoter will downregulated MICA expression. A genome-wide analysis indicates that transcriptional interference between tandem intragenic promoters may be involved in regulating the expression of multiple other human genes.
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Lipp, M., R. Schilling, S. Wiest, G. Laux, and G. W. Bornkamm. "Target sequences for cis-acting regulation within the dual promoter of the human c-myc gene." Molecular and Cellular Biology 7, no. 4 (April 1987): 1393–400. http://dx.doi.org/10.1128/mcb.7.4.1393-1400.1987.
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Recombinant plasmids of the human c-myc promoter-leader region and the bacterial chloramphenicol acetyltransferase (cat) gene were constructed. After transfection into different rodent and human cells, the 862-base-pair (bp) PvuII fragment carrying both c-myc promoters and 350 bp of the untranslated leader conferred 1/15 to 1/30 of the CAT activity mediated by the simian virus 40 promoter. The presence of additional sequences upstream of the PvuII fragment had an overall negative effect on c-myc promoter activity detectable by titration analysis with small amounts of transfected plasmid DNA. The analysis of numerous deletion constructs in the c-myc promoter-leader region as well as S1 mapping experiments demonstrated that the high CAT activity depended largely on the presence of the second promoter. By cotransfection of c-myc-cat constructs with plasmids carrying different parts of the c-myc promoter locus, targets for positively acting cellular factors were identified. Two positive regulatory elements were mapped within the 862-bp PvuII fragment. One was localized within the 248-bp PvuII-SmaI fragment -101 to -349 bp upstream of the first cap site and the other within the 142-pb XhoI-NaeI fragment of the first exon, comprising positions -95 to +47 relative to the second cap site. We conclude that the dual promotor of the human c-myc gene represents a strong eucaryotic promotor regulated by cooperation of positively and negatively acting cellular transcription factors.
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Lipp, M., R. Schilling, S. Wiest, G. Laux, and G. W. Bornkamm. "Target sequences for cis-acting regulation within the dual promoter of the human c-myc gene." Molecular and Cellular Biology 7, no. 4 (April 1987): 1393–400. http://dx.doi.org/10.1128/mcb.7.4.1393.
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Recombinant plasmids of the human c-myc promoter-leader region and the bacterial chloramphenicol acetyltransferase (cat) gene were constructed. After transfection into different rodent and human cells, the 862-base-pair (bp) PvuII fragment carrying both c-myc promoters and 350 bp of the untranslated leader conferred 1/15 to 1/30 of the CAT activity mediated by the simian virus 40 promoter. The presence of additional sequences upstream of the PvuII fragment had an overall negative effect on c-myc promoter activity detectable by titration analysis with small amounts of transfected plasmid DNA. The analysis of numerous deletion constructs in the c-myc promoter-leader region as well as S1 mapping experiments demonstrated that the high CAT activity depended largely on the presence of the second promoter. By cotransfection of c-myc-cat constructs with plasmids carrying different parts of the c-myc promoter locus, targets for positively acting cellular factors were identified. Two positive regulatory elements were mapped within the 862-bp PvuII fragment. One was localized within the 248-bp PvuII-SmaI fragment -101 to -349 bp upstream of the first cap site and the other within the 142-pb XhoI-NaeI fragment of the first exon, comprising positions -95 to +47 relative to the second cap site. We conclude that the dual promotor of the human c-myc gene represents a strong eucaryotic promotor regulated by cooperation of positively and negatively acting cellular transcription factors.
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Rosado-Castellano, Fátima, and Nieves Martín-Bermúdez. "Relación familia-escuela como impulsora de la Educación para la Salud. Análisis de la legislación educativa." Educational journal ESAMEC, no. 1 (2020): 56–65. http://dx.doi.org/10.12795/esamec.2020.i01.07.
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El presente trabajo se muestra como un estudio teórico nacido de la necesidad de estudiar la relación existente entre dos ámbitos importantes para la vida de la persona, escuela y familia, y estos como impulsores de la Educación para la Salud. Para conocer las posibilidades participativas de la familia en la escuela y la inclusión de la Educación para la Salud se aborda un análisis de contenido legislativo en materia educativa que se encuentra vigente en la actualidad tanto a nivel nacional como autonómico, en su caso en Extremadura. Los resultados arrojan que la relación familia-escuela se configura como un entramado favorecedor para la obtención de logros educativos tanto en la infancia como en la adolescencia considerándose la Educación para la Salud una disciplina trasversal que abordar curricularmente, contando con la participación de todos los agentes implicados. Como conclusión se destaca que el binomio familia-escuela es un pilar básico para la educación integral
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Kurata, Lehlohonolo, Setho J. Mokhets’engoane, and ’Mampota Selialia. "Content Analysis of LGCSE Religious Studies Syllabus: To What Extend Does It Address the 21st Century Skills?" European Journal of Education and Pedagogy 3, no. 6 (December 7, 2022): 178–84. http://dx.doi.org/10.24018/ejedu.2022.3.6.495.
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Recently, there has been renewed interest of countries to reform their curriculum in order to promote 21st century skills among learners. It is expected too, that subject syllabi should align with the curriculum in promoting such skills. However, most studies in the field of religious studies in Lesotho have not focused on the extent to which this subject contributes to the promotion of 21st century skills and that prompted the present study. Qualitative Content Analysis was employed to determine the extent to which religious studies syllabus promotes 21st century skills. Document Analysis was used to analyze aims of the syllabus to establish different skills which are promoted by each aim. The findings indicated that religious studies syllabus aims differ in terms of the degree at which they promote 21st century skills. It also appeared that learning and innovation skills are predominantly promoted by the syllabus aims. However, the syllabus’ aims seem to shrink from promoting technological skills. As a result, the following suggestions were made; first, the curriculum developers should emphasize all skills equivalently. Additionally, curriculum developers should restructure the curriculum to promote technological skills.
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Jores, Tobias, Jackson Tonnies, Travis Wrightsman, Edward S. Buckler, Josh T. Cuperus, Stanley Fields, and Christine Queitsch. "Synthetic promoter designs enabled by a comprehensive analysis of plant core promoters." Nature Plants 7, no. 6 (June 2021): 842–55. http://dx.doi.org/10.1038/s41477-021-00932-y.
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Martin, Craig T., and Joseph E. Coleman. "Kinetic analysis of T7 RNA polymerase-promoter interactions with small synthetic promoters." Biochemistry 26, no. 10 (May 19, 1987): 2690–96. http://dx.doi.org/10.1021/bi00384a006.
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Khatamirad, Mohammad, Martin Konrad, Manuel Gentzen, Chiara Boscagli, Christian Almer, Aleks Arinchtein, Michael Geske, Frank Rosowski, and Ralph Kraehnert. "A Systematic Approach to Study Complex Ternary Co-Promoter Interactions: Addition of Ir, Li, and Ti to RhMn/SiO2 for Syngas Conversion to Ethanol." Catalysts 12, no. 11 (October 27, 2022): 1321. http://dx.doi.org/10.3390/catal12111321.
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The direct conversion of synthesis gas could open up economically viable routes for the efficient production of ethanol. RhMn/SiO2 represents one of the most active systems reported thus far. Potential improvements were reported by added dopants, i.e., Ir, Ti, and Li. Yet, combining these elements leads to contradicting results, owing to the complexity of the interactions in a multi-promoted system. This complexity is often encountered in heterogeneous catalysis. We report a systematic data-driven approach for the assessment of complex multi-promoter interactions based on a combination of design-of-experiment, high-throughput experimentation, statistical analysis, and mechanistic assessment. We illustrate this approach for the system RhMn/SiO2 promoted with Ir, Li, and Ti. Using this approach, we investigate the impact of promoters’ interactions on a mechanistic level. Our analysis depicts the means to learn hidden correlations in the performance data and, additionally, high performance for ethanol yield for the RhMnIr/SiO2 catalyst. The method presented outlines an efficient way to also elucidate co-promoter interactions in other complex environments.
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Sajib, Abdul Mohin, Maninder Sandey, Samantha Morici, Bradley Schuler, Payal Agarwal, and Bruce F. Smith. "Analysis of endogenous and exogenous tumor upregulated promoter expression in canine tumors." PLOS ONE 15, no. 11 (November 9, 2020): e0240807. http://dx.doi.org/10.1371/journal.pone.0240807.
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Gene therapy is a promising treatment option for cancer. However, its utility may be limited due to expression in off-target cells. Cancer-specific promoters such as telomerase reverse transcriptase (TERT), survivin, and chemokine receptor 4 (CXCR4) have enhanced activity in a variety of human and murine cancers, however, little has been published regarding these promoters in dogs. Given the utility of canine cancer models, the activity of these promoters along with adenoviral E2F enhanced E1a promoter (EEE) was evaluated in a variety of canine tumors, both from the endogenous gene and from exogenously administered constructs. Endogenous expression levels were measured for cTERT, cSurvivin, and cCXCR4 and were low for all three, with some non-malignant and some tumor cell lines and tissues expressing the gene. Expression levels from exogenously supplied promoters were measured by both the number of cells expressing the construct and the intensity of expression in individual cells. Exogenously supplied promoters were active in more cells in all tumor lines than in normal cells, with the EEE promoter being most active, followed by cTERT. The intensity of expression varied more with cell type than with specific promoters. Ultimately, no single promoter was identified that would result in reliable expression, regardless of the tumor type. Thus, these findings imply that identification of a pan-cancer promoter may be difficult. In addition, this data raises the concern that endogenous expression analysis may not accurately predict exogenous promoter activity.
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Meng, Wei, Arnab Chakravarti, and Tim Lautenschlaeger. "Methylation-specific high-resolution melting analysis (MS-HRM)-based DNA promoter profiling in paired FFPE bladder cancer samples." Journal of Clinical Oncology 30, no. 5_suppl (February 10, 2012): 315. http://dx.doi.org/10.1200/jco.2012.30.5_suppl.315.
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315 Background: DNA methylation and histone modification are widely studied epigenetic events that can decrease gene expression levels. Promoter hypermethylation has been proposed as a potential diagnostic or prognostic biomarker in various cancers. We studied DNA promoter methylation of 5 cancer-associated genes (MRE11, APX1, ERCC1, RASSF1A and RASSF2A ) in paired FFPE bladder cancer tissues and normal adjacent tissue. The MRE11/Rad50/NBS1 complex serves as a single-strand DNA nuclease which participates in the repair of DNA double-strand breaks and replication errors. APX1 plays a key role in regulating H2O2 levels and H2O2 signaling. DNA repair machinery, ERCC1 protein levels in tumor tissue have been shown to predict response to platinum-based chemotherapy. RASSF1 is thought to be a tumor suppressor gene, while the function of RASSF2 is less well understood. Methods: 16 bladder cancer cases with available paraffin-embedded tumor and matched normal adjacent tissue specimens (32 tissue samples) were analyzed. DNA was extracted by Ambion RecoverAll Total Nucleic Acid Isolation kit. FFPE DNA bisulfite modification was performed using Zymo EZ DNA Methylation Kit. Methylation Specific-High Resolution Melting (MS-HRM) analysis was used to assess methylation status. MS-HRM monitors the melting behavior of PCR amplicons by using a DNA intercalating fluorescent dye. Results: MRE11 and APX1 promoters were not methylated in either cancer or normal adjacent samples. The ERCC1 gene was heavily methylated in 94% (30/32) of all cancer and wild type samples. RASSF1A and RASSF2A promoter methylation was significantly different between cancer and normal adjacent tissue. 50% (8/16) RASSF1A and 25% (4/16) RASSF2A had promoter methylation in cancer tissues, while only 6% (1/16) RASSF1A and 0% (0/16) RASSF2A had promoter methylation in normal adjacent tissues. 69% (11/16) of bladder cancer tissues were positive for RASSF1A or RASSF2A promotor methylation while only 1/16 normal adjacent tissue samples was positive for either promotor methylation. Conclusions: The results show that cancer and non-cancer tissue have different RASSF1A and RASSF2A promoter methylation patterns.
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Ponticelli, A. S., and K. Struhl. "Analysis of Saccharomyces cerevisiae his3 transcription in vitro: biochemical support for multiple mechanisms of transcription." Molecular and Cellular Biology 10, no. 6 (June 1990): 2832–39. http://dx.doi.org/10.1128/mcb.10.6.2832-2839.1990.
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The promoter region of the Saccharomyces cerevisiae his3 gene contains two TATA elements, TC and TR, that direct transcription initiation to two sites designated +1 and +13. On the basis of differences between their nucleotide sequences and their responsiveness to upstream promoter elements, it has previously been proposed that TC and TR promote transcription by different molecular mechanisms. To begin a study of his3 transcription in vitro, we used S. cerevisiae nuclear extracts together with various DNA templates and transcriptional activator proteins that have been characterized in vivo. We demonstrated accurate transcription initiation in vitro at the sites used in vivo, transcriptional activation by GCN4, and activation by a GAL4 derivative on various gal-his3 hybrid promoters. In all cases, transcription stimulation was dependent on the presence of an acidic activation region in the activator protein. In addition, analysis of promoters containing a variety of TR derivatives indicated that the level of transcription in vitro was directly related to the level achieved in vivo. The results demonstrated that the in vitro system accurately reproduced all known aspects of in vivo his3 transcription that depend on the TR element. However, in striking contrast to his3 transcription in vivo, transcription in vitro yielded approximately 20 times more of the +13 transcript than the +1 transcript. This result was not due to inability of the +1 initiation site to be efficiently utilized in vitro, but rather it reflects the lack of TC function in vitro. The results support the idea that TC and TR mediate transcription from the wild-type promoter by distinct mechanisms.
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Ponticelli, A. S., and K. Struhl. "Analysis of Saccharomyces cerevisiae his3 transcription in vitro: biochemical support for multiple mechanisms of transcription." Molecular and Cellular Biology 10, no. 6 (June 1990): 2832–39. http://dx.doi.org/10.1128/mcb.10.6.2832.
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The promoter region of the Saccharomyces cerevisiae his3 gene contains two TATA elements, TC and TR, that direct transcription initiation to two sites designated +1 and +13. On the basis of differences between their nucleotide sequences and their responsiveness to upstream promoter elements, it has previously been proposed that TC and TR promote transcription by different molecular mechanisms. To begin a study of his3 transcription in vitro, we used S. cerevisiae nuclear extracts together with various DNA templates and transcriptional activator proteins that have been characterized in vivo. We demonstrated accurate transcription initiation in vitro at the sites used in vivo, transcriptional activation by GCN4, and activation by a GAL4 derivative on various gal-his3 hybrid promoters. In all cases, transcription stimulation was dependent on the presence of an acidic activation region in the activator protein. In addition, analysis of promoters containing a variety of TR derivatives indicated that the level of transcription in vitro was directly related to the level achieved in vivo. The results demonstrated that the in vitro system accurately reproduced all known aspects of in vivo his3 transcription that depend on the TR element. However, in striking contrast to his3 transcription in vivo, transcription in vitro yielded approximately 20 times more of the +13 transcript than the +1 transcript. This result was not due to inability of the +1 initiation site to be efficiently utilized in vitro, but rather it reflects the lack of TC function in vitro. The results support the idea that TC and TR mediate transcription from the wild-type promoter by distinct mechanisms.
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Qazi, Sarah Rizwan, Noor ul Haq, Shakeel Ahmad, and Samina N. Shakeel. "HSEAT: A Tool for Plant Heat Shock Element Analysis, Motif Identification and Analysis." Current Bioinformatics 15, no. 3 (May 23, 2020): 196–203. http://dx.doi.org/10.2174/1574893614666190102151956.
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Background: Previous methods used to discover cis-regulatory motifs in promoter region of plant genes possess very limited performance, especially for analysis of novel and rare motifs. Different plant genes have differential expression under different environmental or experimental conditions and modular regulation of cis-regulatory sequences in promoter regions of the same or different genes. It has previously been revealed that Heat Shock Proteins (HSPs) creation is correlated with plant tolerance under heat and other stress conditions. Regulation of these HSP genes is controlled by interactions between heat shock factors (HSFs) with cis-acting motifs present in the promoter region of the genes. Differential expression of these HSP genes is because of their unique promoter architecture, cis-acting sequences and their interaction with HSFs. Objective: A versatile promoter analysis tool was proposed for identification and analysis of promoters of HSPs. Methods: Heat Shock Element Analysis Tool (HSEAT) has been implemented in java programming language using pattern recognition approach. This tool has build-in MS access database for storing different motifs. Results: HSEAT has been designed to detect different types of Heat Shock Elements (HSEs) in promoter regions of plant HSPs with integration of complete analysis of plant promoters to the tool. HSEAT is user-friendly, interactive application to discover various types of HSEs e.g. TTC Rich Types, Gap Types and Prefect HSE as well as STRE in HSPs. Here we examined and evaluated some known HSP promoters from different plants using this tool with already available tools. Conclusion: HSEAT has extensive potential to explore conserved or semi-conserved motifs or potential binding sites of different transcription factors for other stress regulating genes. This tool can be found at https://sourceforge.net/projects/heast/.
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Efremova, Larisa N., Svetlana R. Strelnikova, Guzel R. Gazizova, Elena A. Minkina, and Roman A. Komakhin. "A Synthetic Strong and Constitutive Promoter Derived from the Stellaria media pro-SmAMP1 and pro-SmAMP2 Promoters for Effective Transgene Expression in Plants." Genes 11, no. 12 (November 26, 2020): 1407. http://dx.doi.org/10.3390/genes11121407.
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Synthetic promoters are vital for genetic engineering-based strategies for crop improvement, but effective methodologies for their creation and systematic testing are lacking. We report here on the comparative analysis of the promoters pro-SmAMP1 and pro-SmAMP2 from Stellaria media ANTIMICROBIAL PEPTIDE1 (AMP1) and ANTIMICROBIAL PEPTIDE2 (AMP2). These promoters are more effective than the well-known Cauliflower mosaic virus 35S promoter. Although these promoters share about 94% identity, the pro-SmAMP1 promoter demonstrated stronger transient expression of a reporter gene in Agrobacterium infiltration of Nicotiana benthamiana leaves, while the pro-SmAMP2 promoter was more effective for the selection of transgenic tobacco (Nicotiana tabacum) cells when driving a selectable marker. Using the cap analysis of gene expression method, we detected no differences in the structure of the transcription start sites for either promoter in transgenic plants. For both promoters, we used fine-scale deletion analysis to identify 160 bp-long sequences that retain the unique properties of each promoter. With the use of chimeric promoters and directed mutagenesis, we demonstrated that the superiority of the pro-SmAMP1 promoter for Agrobacterium-mediated infiltration is caused by the proline-inducible ACTCAT cis-element strictly positioned relative to the TATA box in the core promoter. Surprisingly, the ACTCAT cis-element not only activated but also suppressed the efficiency of the pro-SmAMP1 promoter under proline stress. The absence of the ACTCAT cis-element and CAANNNNATC motif (negative regulator) in the pro-SmAMP2 promoter provided a more constitutive gene expression profile and better selection of transgenic cells on selective medium. We created a new synthetic promoter that enjoys high effectiveness both in transient expression and in selection of transgenic cells. Intact promoters with differing properties and high degrees of sequence identity may thus be used as a basis for the creation of new synthetic promoters for precise and coordinated gene expression.
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KANAYA, SHIGEHIKO, and YOSHIHIRO KUDO. "STATISTICAL EXAMINATION OF DISSIMILARITY OF PROMOTER AND PROMOTER-LIKE SEQUENCES IN ESCHERICHIA COLI." Analytical Sciences 7, Supple (1991): 739–42. http://dx.doi.org/10.2116/analsci.7.supple_739.
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Joshi, B., S. Rastogi, M. Morris, L. M. Carastro, C. Decook, E. Seto, and S. P. Chellappan. "Differential regulation of human YY1 and caspase 7 promoters by prohibitin through E2F1 and p53 binding sites." Biochemical Journal 401, no. 1 (December 11, 2006): 155–66. http://dx.doi.org/10.1042/bj20060364.
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Prohibitin is a 30 kDa growth suppressive protein that has pleiotropic functions in the cell. Although prohibitin has been demonstrated to have potent transcriptional regulatory functions, it has also been proposed to facilitate protein folding in the mitochondria and promote cell migration in association with Raf-1. Our previous studies have shown that prohibitin physically interacts with the marked-box domain of E2F family members and represses their transcriptional activity; in contrast, prohibitin could bind to and enhance the transcriptional activity of p53. Here, we show that promoters of human YY1 (Yin and Yang 1) as well as caspase 7 genes are modulated by prohibitin. YY1 promoter activity was reduced upon overexpression of prohibitin, while it was enhanced when prohibitin was depleted by small interfering RNA techniques. The repressive effects of prohibitin on the YY1 promoter were mediated through E2F binding sites, as seen by mutational analysis and chromatin immunoprecipitation assays. Further, depletion of E2F1 prevented prohibitin from repressing the YY1 promoter. In contrast with YY1, prohibitin overexpression led to enhanced levels of caspase 7, whereas depletion of prohibitin reduced it. Interestingly, the caspase 7 promoter was found to have p53-binding sites and prohibitin activated this promoter through p53. These studies show that prohibitin can have diverse effects on the expression of different genes and the activity of various cellular promoters is affected by prohibitin. Further, it appears very likely that prohibitin carries out many of its cellular functions by affecting the transcription of different genes.
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Valladares, Ana, Alicia M. Muro-Pastor, Antonia Herrero, and Enrique Flores. "The NtcA-Dependent P1 Promoter Is Utilized for glnA Expression in N2-Fixing Heterocysts of Anabaena sp. Strain PCC 7120." Journal of Bacteriology 186, no. 21 (November 1, 2004): 7337–43. http://dx.doi.org/10.1128/jb.186.21.7337-7343.2004.
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ABSTRACT Expression of the glnA gene encoding glutamine synthetase, a key enzyme in nitrogen metabolism, is subject to a variety of regulatory mechanisms in different organisms. In the filamentous, N2-fixing cyanobacterium Anabaena sp. strain PCC 7120, glnA is expressed from multiple promoters that generate several transcripts whose abundance is influenced by NtcA, the transcription factor exerting global nitrogen control in cyanobacteria. Whereas RNAI originates from a canonical NtcA-dependent promoter (P1) and RNAII originates from a σ70-type promoter (P2), RNAIV is influenced by NtcA but the corresponding promoter (P3) does not have the structure of NtcA-activated promoters. Using RNA isolated from Anabaena filaments grown under different nitrogen regimens, we observed, in addition to these transcripts, RNAV, which has previously been detected only in in vitro transcription assays and should originate from P4. However, in heterocysts, which are differentiated cells specialized in N2 fixation, RNAI was the almost exclusive glnA transcript. Analysis of P glnA ::lacZ fusions containing different fragments of the glnA upstream region confirmed that fragments carrying P1, P2, or P3 and P4 have the ability to promote transcription. Mutation of the NtcA-binding site in P1 eliminated P1-directed transcription and allowed increased use of P2. The NtcA-binding site in the P1 promoter and binding of NtcA to this site appear to be key factors in determining glnA gene expression in vegetative cells and heterocysts.
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van der Straten, Ariane, Rosette Loriau, Albert Herzog, and Alex Bollen. "The α2 cDNA sequence of human haptoglobin carries a bacterial promoter functional in vivo." Bioscience Reports 6, no. 4 (April 1, 1986): 363–73. http://dx.doi.org/10.1007/bf01116423.
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Various constructions of human haptoglobin (Hp) cDNA coding either for the complete α2FSβ precursor protein or only for the β subunit have been placed under the control of the λPR promoter in the bacterial expression vector pCQV2 (Queen, 1983). In addition to the expected 45,000 dalton polypeptide synthesized after induction of the PR promoter, the complete α2FSβ constructions constitutively express a smaller polypeptide of ∼30,000 dalton corresponding to a truncated Hp protein. Computer analysis of the HpcDNA revealed the presence of two strong potential bacterial promoters (α2PF and α2PS) located in the duplicated α2FS sequence. Both Hp promoter signals are followed by potential mRNA start sites and ribosome binding sites at a compatible distance from initiation codons. In addition, the Hpα2 cDNA sequence, when fused upstream to the cDNA coding for α1-antitrypsin, constitutively promotes in vivo the efficient expression of an hybrid protein specifically recognized by antibodies raised against α1-antitrypsin or haptoglobin.
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McLean, Bradley W., Shari L. Wiseman, and Andrew M. Kropinski. "Functional analysis of sigma-70 consensus promoters in Pseudomonas aeruginosa and Escherichia coli." Canadian Journal of Microbiology 43, no. 10 (October 1, 1997): 981–85. http://dx.doi.org/10.1139/m97-141.
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A series of synthetic promoters, based upon the Escherichia coli σ70 consensus promoter sequence, was constructed upstream of the lacZ reporter gene in the modified broad-host-range vector pQF52. The role of the intervening spacer region in gene expression in Pseudomonas aeruginosa and E. coli was studied by insertions and deletions within this region. In P. aeruginosa and E. coli the patterns of gene expression were identical with maximum β-galactosidase activity being measured from promoters possessing 19 bp in their intervening regions, presumably as a result of impeded promoter clearance with the consensus 17-bp promoter. In P. aeruginosa a second occurrence of enhanced activity, which could not be attributed to the involvement of the alternative sigma factor RpoN (σ54), was evident with the promoter having a 16-bp spacer.Key words: Pseudomonas aeruginosa, promoter, RpoD, RpoN, transcription.
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González Velastín, Rodrigo. "Social policy and the production of age norms for later life: The case of ageing policies in Chile." International Journal of Ageing and Later Life 13, no. 1 (April 8, 2019): 5–33. http://dx.doi.org/10.3384/ijal.1652-8670.17373.
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Social policies have been recognised as guiding narratives that promote and legitimise certain models of ageing. This finding, however, has been achieved by studies focussed on the reality of developed countries. Furthermore, little is known about how social policies promote age norms for later life in the context of developing countries. This research addresses this knowledge gap and focusses on the Chilean case, paying particular attention to what age norms are promoted by the two national ageing policies implemented by this country in 1996 and 2012. A critical discourse analysis method was used to identify the ways in which each policy conceptualises ageing as a social problem and the prescriptive behaviours and expectations that each policy promotes regarding old age. Results indicate that a rhetorical evolution can be observed in the analysed period, as each policy promotes different later life depictions and social norms.
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Harr, Michael W., Xinyang Zhao, Mary Klein, Fan Liu, Megan Hatlen, and Stephen Nimer. "JAK2 V617F, PRMT5, and GATA-1 Form a Regulatory Loop That Controls Autophagy Via Effects on ATG3 Gene Expression." Blood 118, no. 21 (November 18, 2011): 2822. http://dx.doi.org/10.1182/blood.v118.21.2822.2822.
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Abstract Abstract 2822 The JAK2 V617F mutation is the most prevalent genetic abnormality in Philadelphia chromosome negative myeloproliferative neoplasia. We recently discovered that JAK2 V617F phosphorylates and inactivates PRMT5, a type II arginine methyltransferase that promotes transcriptional repression. To evaluate the PRMT5 dependent and independent effects of JAK2 V617F, we performed microarray analysis of human erythroleukemia cells (homozygous for JAK2 V617F) treated with a JAK2 inhibitor or transduced with PRMT5 shRNA. We discovered 5 autophagy-related genes (ATG3, ATG7, ATG2B, ATG5, and ATG16L1) that were positively regulated by JAK2 V617F, but negatively regulated by PRMT5. PRMT5 was bound to the promoters of these genes and binding was enhanced when PRMT5 was re-activated by a JAK2 inhibitor. Sequence analysis of ATG promoters identified at least one potential GATA-1 binding site in each ATG gene. Yet, knock-down of GATA-1 decreased the expression of ATG3 (by approximately 50%), but not the other ATG genes. ChIP analysis identified binding of both GATA-1 and PRMT5 to the ATG3 promoter, which suggests that ATG3 is transcriptionally induced by GATA-1 when PRMT5 is inactivated by JAK2 V617F. But when PRMT5 was active, it was bound to the GATA-1 promoter and ATG3 expression was downregulated. As JAK2 V617F (but not wild type) induces ATG3 expression and autophagy in AML cells and ATG3 levels are elevated in CD34+ cells from polycythemia vera patients, we conclude that JAK2 V617F promotes autophagy by inactivating PRMT5 and promoting GATA-1-dependent transcription of ATG3. Targeting autophagy with JAK2 inhibitors or other agents may be efficacious in the treatment of myeloproliferative neoplasia. Disclosures: No relevant conflicts of interest to declare.
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Li, Yan, Caihua Dong, Ming Hu, Zetao Bai, Chaobo Tong, Rong Zuo, Yueying Liu, et al. "Identification of Flower-Specific Promoters through Comparative Transcriptome Analysis in Brassica napus." International Journal of Molecular Sciences 20, no. 23 (November 26, 2019): 5949. http://dx.doi.org/10.3390/ijms20235949.
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Brassica napus (oilseed rape) is an economically important oil crop worldwide. Sclerotinia stem rot (SSR) caused by Sclerotinia sclerotiorum is a threat to oilseed rape production. Because the flower petals play pivotal roles in the SSR disease cycle, it is useful to express the resistance-related genes specifically in flowers to hinder further infection with S. sclerotiorum. To screen flower-specific promoters, we first analyzed the transcriptome data from 12 different tissues of the B. napus line ZS11. In total, 249 flower-specific candidate genes with high expression in petals were identified, and the expression patterns of 30 candidate genes were verified by quantitative real-time transcription-PCR (qRT-PCR) analysis. Furthermore, two novel flower-specific promoters (FSP046 and FSP061 promoter) were identified, and the tissue specificity and continuous expression in petals were determined in transgenic Arabidopsis thaliana with fusing the promoters to β-glucuronidase (GUS)-reporter gene. GUS staining, transcript expression pattern, and GUS activity analysis indicated that FSP046 and FSP061 promoter were strictly flower-specific promoters, and FSP046 promoter had a stronger activity. The two promoters were further confirmed to be able to direct GUS expression in B. napus flowers using transient expression system. The transcriptome data and the flower-specific promoters screened in the present study will benefit fundamental research for improving the agronomic traits as well as disease and pest control in a tissue-specific manner.
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Eder, Steve, Wei Liu, and F. Marion Hulett. "Mutational Analysis of the phoD Promoter in Bacillus subtilis: Implications for PhoP Binding and Promoter Activation of Pho Regulon Promoters." Journal of Bacteriology 181, no. 7 (April 1, 1999): 2017–25. http://dx.doi.org/10.1128/jb.181.7.2017-2025.1999.
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ABSTRACT The PhoP-PhoR two-component regulatory system controls the phosphate deficiency response in B. subtilis. A number of Pho regulon genes which require PhoP∼P for activation or repression have been identified. The studies reported here were initiated to understand the PhoP-DNA interaction necessary for Pho promoter regulation. The regulatory region of phoD was characterized in detail using oligo-directed mutagenesis, DNase I footprinting, and in vivo transcription assays. These data reveal basic principles of PhoP binding relevant to PhoP’s interaction with other Pho regulon promoters. Our results show that: (i) a dimer of PhoP∼P is able to bind two consensus repeats in a stable fashion; (ii) PhoP binding is highly cooperative within the core promoter region, which is located from −66 to −17 on the coding strand and contains four TT(A/T/C)ACA-like repeats; (iii) specific bases comprising the TT(A/T/C)ACA consensus are essential for transcriptional activation, but the specific base pairs of the intervening sequences separating the consensus repeats are not important for either PhoP binding or promoter activation; (iv) the spacing between two consensus repeats within a putative dimer binding site in the core region is important for both PhoP binding and promoter activation; (v) the exact spacing between two dimer binding sites within the core region is important for promoter activation but less so for PhoP binding affinity, as long as the repeats are on the same face of the helix; and (vi) the 5′ secondary binding region is important for coordinated PhoP binding to the core binding region, making it nearly essential for promoter activation.
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Yu, Peng, Jun Li, Bingshen Jia, Zizhenbiao Wang, Sheng Wang, and Kun Fu. "Experimental Study on the Construction of Tissue Engineered Bone by Bone Marrow Mesenchymal Stem Cells Induced by MiR-29b Composite Bionic Scaffold." Journal of Biomaterials and Tissue Engineering 9, no. 12 (December 1, 2019): 1763–69. http://dx.doi.org/10.1166/jbt.2019.2195.
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MiR-29b promotes osteogenic differentiation of bone marrow mesenchymal stem cells (BMSCs). Our study aims to evaluate MiR-29b's role in composite bionic scaffold-induced BMSCs in the construction of tissue engineered bone. Rat BMSCs were isolated and transfected with NC (negative control) and MiR-29b plasmid. Cell proliferation was assessed by MTT assay and the expression of osteogenic genes Runx2 and OC was analyzed by Real time PCR. Healthy male SD rats were divided into fracture group; negative control group; and MiR-29b group followed by analysis of the changes of bone mineral density, ALP activity, and expression of MiR-29b, type I collagen and Runx2 by Real time PCR. Up-regulation of MiR-29b significantly promoted BMSCs cell proliferation, inhibited Caspase 3 activity, and promoted Runx2 and OC expression compared to NC group (P < 0 05). NC group showed significantly increased bone density, ALP activity and the expression of type I collagen and Runx2 compared with control group (P < 0 05). Transfection of BMSCs induced by MiR-29b combined with biomimetic scaffold significantly promoted the expression of MiR-29b in fractured rats, increased bone mineral density and ALP activity, as well as upregulated type I collagen and Runx2, compared to NC group (P < 0 05). Up-regulation of MiR-29b promotes cell proliferation and osteogenic differentiation of BMSCs. Implantation of BMSCs induced by MiR-29b composite bionic scaffold can promote osteogenic differentiation and promote bone healing in bone defects.
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Wang, Benqi, Jie Liu, Lei Chu, Xue Jing, Huadong Wang, Jian Guo, and Bin Yi. "Exogenous Promoter Triggers APETALA3 Silencing through RNA-Directed DNA Methylation Pathway in Arabidopsis." International Journal of Molecular Sciences 20, no. 18 (September 11, 2019): 4478. http://dx.doi.org/10.3390/ijms20184478.
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The development of floral organs plays a vital role in plant reproduction. In our research, the APETALA3 (AP3) promoter-transgenic lines showed abnormal developmental phenotypes in stamens and petals. The aim of this study is to understand the molecular mechanisms of the morphological defects in transgenic plants. By performing transgenic analysis, it was found that the AP3-promoted genes and the vector had no relation to the morphological defects. Then, we performed the expression analysis of the class A, B, and C genes. A dramatic reduction of transcript levels of class B genes (AP3 and PISTILLATA) was observed. Additionally, we also analyzed the methylation of the promoters of class B genes and found that the promoter of AP3 was hypermethylated. Furthermore, combining mutations in rdr2-2, drm1/2, and nrpd1b-11 with the AP3-silencing lines rescued the abnormal development of stamens and petals. The expression of AP3 was reactivated and the methylation level of AP3 promoter was also reduced in RdDM-defective AP3-silencing lines. Our results showed that the RdDM pathway contributed to the transcriptional silencing in the transgenic AP3-silencing lines. Moreover, the results revealed that fact that the exogenous fragment of a promoter could trigger the methylation of homologous endogenous sequences, which may be ubiquitous in transgenic plants.
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Lv, Wu-Hong, Guang-Hui Chen, Mei-Qin Zhuo, Yi-Huan Xu, Yi-Chuang Xu, and Xiao-Ying Tan. "Functional Analysis of Steroidogenic Factor 1 (sf-1) and 17α-Hydroxylase/Lyase (cyp17α) Promoters in Yellow Catfish Pelteobagrus fulvidraco." International Journal of Molecular Sciences 22, no. 1 (December 27, 2020): 195. http://dx.doi.org/10.3390/ijms22010195.
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The present study was performed to clone and characterize the structures and functions of steroidogenic factor 1 (sf-1) and 17α-hydroxylase/lyase (cyp17α) promoters in yellow catfish Pelteobagrus fulvidraco, a widely distributed freshwater teleost. We successfully obtained 1981 and 2034 bp sequences of sf-1 and cyp17α promoters, and predicted the putative binding sites of several transcription factors, such as Peroxisome proliferator-activated receptor alpha (PPARα), Peroxisome proliferator-activated receptor gamma (PPARγ) and Signal transducer and activator of transcription 3 (STAT3), on sf-1 and cyp17α promoter regions, respectively. Overexpression of PPARγ significantly increased the activities of sf-1 and cyp17α promoters, but overexpression of PPARα significantly decreased the promoter activities of sf-1 and cyp17α. Overexpression of STAT3 reduced the activity of the sf-1 promoter but increased the activity of the cyp17α promoter. The analysis of site-mutation and electrophoretic mobility shift assay suggested that the sf-1 promoter possessed the STAT3 binding site, but did not the PPARα or PPARγ binding sites. In contrast, only the PPARγ site, not PPARα or STAT3 sites, was functional with the cyp17α promoter. Leptin significantly increased sf-1 promoter activity, but the mutation of STAT3 and PPARγ sites decreased leptin-induced activation of sf-1 promoter. Our findings offered the novel insights into the transcriptional regulation of sf-1 and cyp17α and suggested leptin regulated sf-1 promoter activity through STAT3 site in yellow catfish.
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Manna, Adhar C., Manfred G. Bayer, and Ambrose L. Cheung. "Transcriptional Analysis of Different Promoters in the sar Locus in Staphylococcus aureus." Journal of Bacteriology 180, no. 15 (August 1, 1998): 3828–36. http://dx.doi.org/10.1128/jb.180.15.3828-3836.1998.
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ABSTRACT The expression of extracellular virulence determinants inStaphylococcus aureus is controlled by a 510-nucleotide RNA molecule (RNAIII) which is a part of theagr system. The agr operon, which encodes a multicomponent signal transduction system, is partially under the influence of an unlinked regulatory locus calledsar. The sar locus is composed of three overlapping transcripts, designated sarA (0.56 kb),sarC (0.8 kb), and sarB (1.2 kb), originating from the P1, P3, and P2 promoters, respectively. In this study, we analyzed the differential expression of these promoters by using transcriptional fusion with the xylE reporter gene to study the activation of the sar locus. The data confirm the existence of three independent promoters with different promoter activities. Maximal promoter activity was observed with the combined fusion of P2-P3-P1 promoters. Expression studies with a sigB mutant revealed that the P3 promoter is SigB dependent. Analysis of these transcriptional fusions in a sarA mutant and in complemented strains with each of the sar transcriptional units revealed that thesar locus is autoregulatory, with SarA acting as a positive regulator. From various transcriptional fusion studies of the upstream region of the P1 promoter, we have localized a 34-bp sequence which seems to play a role in down-modulating P1 transcription. Using heparin-Sepharose and DNA-specific columns, we partially purified a 12-kDa protein, possibly a repressor, which binds to the promoter regions upstream of P2 and P1 and which also binds to the 34-bp sequence. These data indicated that the regulation of thesar locus is complex and may involve the sargene product(s) and other regulatory protein(s).
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Wettstein-Edwards, J., B. S. Ticho, N. C. Martin, D. Najarian, and G. S. Getz. "In vitro transcription and promoter strength analysis of five mitochondrial tRNA promoters in yeast." Journal of Biological Chemistry 261, no. 6 (February 1986): 2905–11. http://dx.doi.org/10.1016/s0021-9258(17)35872-6.
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Masayuki, Yamada, Kubo Motoki, Miyake Toshio, Sakaguchi Reiko, Higo Yuji, and Imanaka Tadayuki. "Promoter sequence analysis in Bacillus and Escherichia: construction of strong promoters in E. coli." Gene 99, no. 1 (March 1991): 109–14. http://dx.doi.org/10.1016/0378-1119(91)90041-9.
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Landry, Josette-Renée, and Dixie L. Mager. "Functional Analysis of the Endogenous Retroviral Promoter of the Human Endothelin B Receptor Gene." Journal of Virology 77, no. 13 (July 1, 2003): 7459–66. http://dx.doi.org/10.1128/jvi.77.13.7459-7466.2003.
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ABSTRACT We previously reported that the long terminal repeats (LTRs) of retroviral elements belonging to the HERV-E family contribute to the expression of the human apolipoprotein C1 (APOC1) and endothelin B receptor (EDNRB) genes by providing alternative promoters. While both LTRs were shown to promote transcription in vivo and in vitro, their respective activity and tissue specificity appeared to differ even though they shared a high degree of sequence identity. In the present study, we further characterized the promoter of the EDNRB LTR and delineated the regions and motifs required for strong activity. We confirmed the placenta-restricted expression of the LTR by transient transfections and quantitative real-time PCR and determined that the retroviral promoter contributes significantly to the level of EDNRB transcripts in placenta, where chimeric mRNAs were found to represent 15% of overall EDNRB mRNAs. Transient transfection of 5′ deletion constructs in cells of placental origin identified a motif, named LPE1, between positions 111 and 122 of the EDNRB LTR necessary for transcriptional activity. Removal of this region, which contains a putative SP1 binding site, abolished promoter activity. A second enhancing region resides between positions 175 and 215 of the LTR and was termed LPE2. Interestingly, this section contained three binding sites that were not present in the APOC1 LTR due to minor nucleotide differences. The predicted motifs in the EDNRB LTR were found to likely act in symbiosis as modifications to any of the three sites reduced transcription by one-third while alterations to all three eliminated promoter activity. The results from this study illustrate how slight variations in transcriptional regulatory sequences can have a profound effect on promoter activity and demonstrate the complex regulatory effects of human endogenous retrovirus elements on human gene expression.
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Salamon, Daniel, Maria Takacs, Dorina Ujvari, Jörg Uhlig, Hans Wolf, Janos Minarovits, and Hans Helmut Niller. "Protein-DNA Binding and CpG Methylation at Nucleotide Resolution of Latency-Associated Promoters Qp, Cp, and LMP1p of Epstein-Barr Virus." Journal of Virology 75, no. 6 (March 15, 2001): 2584–96. http://dx.doi.org/10.1128/jvi.75.6.2584-2596.2001.
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ABSTRACT Epstein-Barr viral (EBV) latency-associated promoters Qp, Cp, and LMP1p are crucial for the regulated expression of the EBNA and LMP transcripts in dependence of the latency type. By transient transfection and in vitro binding analyses, many promoter elements and transcription factors have previously been shown to be involved in the activities of these promoters. However, the latency promoters have only partially been examined at the nucleotide level in vivo. Therefore, we undertook a comprehensive analysis of in vivo protein binding and CpG methylation patterns at these promoters in five representative cell lines and correlated the results with the known in vitro binding data and activities of these promoters from previous transfection experiments. Promoter activity inversely correlated with the methylation state of promoters, although Qp was a remarkable exception. Novel protein binding data were obtained for all promoters. For Cp, binding correlated well with promoter activity; for LMP1p and Qp, binding patterns looked similar regardless of promoter activity.
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Li, Zhengbo, Feng Deng, Qiaoqiao Zhu, Li Cao, and Yunyan Jiang. "Do the Chinese Government’s Efforts to Make a Low-Carbon Industrial Transition Hinder or Promote the Economic Development? Evidence from Low-Carbon Industrial Parks Pilot Policy." Sustainability 15, no. 1 (December 21, 2022): 77. http://dx.doi.org/10.3390/su15010077.
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Under the background of “peak carbon dioxide emissions” and “carbon neutrality” strategy, it is urgent to explore whether China’s great efforts to continuously promote industrial low-carbon transition can promote high-quality economic development. Taking the implementation of low-carbon industrial parks pilot policy (LIPPP) as a “quasi-natural experiment”, this paper tries to answer this question. The results show that the LIPPP doesn’t significantly promote the sustainable-oriented high-quality development (SHD) of the economy, but mainly boosts the value-oriented high-quality development (VHD), which is characterized by being obviously biased towards the technological progress. The policy effect is more obvious in the central region and cities with a relatively poor natural resource endowment. The mechanism analysis shows that the LIPPP promotes the VHD of the economy through the innovation incentive effect and the capital deepening effect. The technological progress related to the VHD promoted by the LIPPP has a crowding out effect on that of the SHD. In addition, regional innovation, capital deepening, and energy transformation all play a certain role in promoting the SHD, but which is overshadowed by the effect of the VHD promoted by the LIPPP. This paper provides policy implications for China to promote high-quality economic development in the process of low-carbon transition.
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Bashyam, Murali D., and Anil K. Tyagi. "Identification and Analysis of “Extended −10” Promoters from Mycobacteria." Journal of Bacteriology 180, no. 9 (May 1, 1998): 2568–73. http://dx.doi.org/10.1128/jb.180.9.2568-2573.1998.
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ABSTRACT Earlier studies from our laboratory on randomly isolated transcriptional signals of mycobacteria had revealed that the −10 region of mycobacterial promoters and the corresponding binding domain in the major sigma factor are highly similar to their Escherichia coli counterparts. In contrast, the sequences in −35 regions of mycobacterial promoters and the corresponding binding domain in the major sigma factor are vastly different from their E. colicounterparts (M. D. Bashyam, D. Kaushal, S. K. Dasgupta, and A. K. Tyagi, J. Bacteriol. 178:4847–4853, 1996). We have now analyzed the role of the TGN motif present immediately upstream of the −10 region of mycobacterial promoters. Sequence analysis and site-specific mutagenesis of a Mycobacterium tuberculosispromoter and a Mycobacterium smegmatis promoter reveal that the TGN motif is an important determinant of transcriptional strength in mycobacteria. We show that mutation in the TGN motif can drastically reduce the transcriptional strength of a mycobacterial promoter. The influence of the TGN motif on transcriptional strength is also modulated by the sequences in the −35 region. Comparative assessment of these extended −10 promoters in mycobacteria and E. coli suggests that functioning of the TGN motif in promoters of these two species is similar.
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Takeda, Hisashi, Akihiro Yamada, Keisuke Miyauchi, Eiji Masai, and Masao Fukuda. "Characterization of Transcriptional Regulatory Genes for Biphenyl Degradation in Rhodococcus sp. Strain RHA1." Journal of Bacteriology 186, no. 7 (April 1, 2004): 2134–46. http://dx.doi.org/10.1128/jb.186.7.2134-2146.2004.
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ABSTRACT Transcription of the bphA1A2A3A4C1B genes, which are responsible for the conversion of biphenyl and polychlorinated biphenyl to the meta-cleavage products in Rhodococcus sp. strain RHA1, was examined. The bphA1 promoter (P bphA1 ) was identified and was shown to promote transcription induction by biphenyl and ethylbenzene. An 8.8-kb HindIII fragment that promotes transcription induction of P bphA1 in Rhodococcus erythropolis IAM1399 was isolated from the region downstream of bphB by using a reporter plasmid containing P bphA1 . Analysis of the nucleotide sequence of this fragment revealed a set of putative two-component regulatory system genes, which were designated bphS and bphT. Deletion analysis of the 8.8-kb HindIII fragment indicated that bphT is responsible for the basal activation of P bphA1 and that both bphS and bphT are required for the elevated basal activation of and transcriptional induction by biphenyl of P bphA1 . These results support the notion that bphS and bphT encode a sensor kinase and a response regulator, respectively, of a two-component regulatory system. The bphS and bphT genes promote transcriptional induction by a variety of aromatic compounds, including biphenyl, benzene, alkylbenzenes, and chlorinated benzenes. A promoter activity assay and reverse transcription (RT)-PCR analysis revealed a weak constitutive promoter in the adjacent region upstream of bphS. RT-PCR analysis indicated that there is induced transcription of bphA1 through bphT, in which P bphA1 is thought to take part. An insertionally inactivated bphS mutant, SDR1, did not grow on biphenyl. Growth was restored by introduction of an intact bphS gene into SDR1. These results indicate that at least bphS is indispensably responsible for the growth of RHA1 on biphenyl.
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SALIM, SM Muztaba, Tetsuo SAGA, Nobuyuki TANIGUCHI, and Fumihiro OKUMURA. "Experimental analysis of the Control of turbulent intensity in a square channel by the Turbulent Promoter." Proceedings of Conference of Kanto Branch 2004.10 (2004): 563–64. http://dx.doi.org/10.1299/jsmekanto.2004.10.563.
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SOROKIN, ANATOLY A., ALEXANDR A. OSYPOV, TIMUR R. DZHELYADIN, PETR M. BESKARAVAINY, and SVETLANA G. KAMZOLOVA. "ELECTROSTATIC PROPERTIES OF PROMOTER RECOGNIZED BYE. COLIRNA POLYMERASE Eσ70." Journal of Bioinformatics and Computational Biology 04, no. 02 (April 2006): 455–67. http://dx.doi.org/10.1142/s0219720006002077.
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A comparative analysis of electrostatic patterns for 359 σ70-specific promoters and 359 nonpromoter regions on electrostatic map of Escherichia coli genome was carried out. It was found that DNA is not a uniformly charged molecule. There are some local inhomogeneities in its electrostatic profile which correlate with promoter sequences. Electrostatic patterns of promoter DNAs can be specified due to the presence of some distinctive motifs which differ for different promoter groups and may be involved as signal elements in differential recognition of various promoters by the enzyme. Some specific electrostatic elements which are responsible for modulating promoter activities due to ADP-ribosylation of RNA polymerase α-subunit were found in far upstream regions of T4 phage early promoters and E. coli ribosomal promoters.
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Stewart, S. E., and G. S. Roeder. "Transcription by RNA polymerase I stimulates mitotic recombination in Saccharomyces cerevisiae." Molecular and Cellular Biology 9, no. 8 (August 1989): 3464–72. http://dx.doi.org/10.1128/mcb.9.8.3464-3472.1989.
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The recombination-stimulating sequence HOT1 is derived from the ribosomal DNA array of Saccharomyces cerevisiae and corresponds to sequences that promote transcription by RNA polymerase I. When inserted at a chromosomal location outside the ribosomal DNA array, HOT1 stimulates mitotic recombination in the adjacent sequences. To investigate the relationship between transcription and recombination, transcription promoted by HOT1 was directly examined. These studies demonstrated that transcription starts at the RNA polymerase I initiation site in HOT1 and proceeds through the chromosomal sequences in which recombination is enhanced. Linker insertion mutations in HOT1 were generated and assayed for recombination stimulation and for promoter function; this analysis demonstrated that the same sequences are required for both activities. These results indicate that the ability of HOT1 to enhance recombination is related to, and most likely dependent on, its ability to promote transcription.
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Stewart, S. E., and G. S. Roeder. "Transcription by RNA polymerase I stimulates mitotic recombination in Saccharomyces cerevisiae." Molecular and Cellular Biology 9, no. 8 (August 1989): 3464–72. http://dx.doi.org/10.1128/mcb.9.8.3464.
Full textAbstract:
The recombination-stimulating sequence HOT1 is derived from the ribosomal DNA array of Saccharomyces cerevisiae and corresponds to sequences that promote transcription by RNA polymerase I. When inserted at a chromosomal location outside the ribosomal DNA array, HOT1 stimulates mitotic recombination in the adjacent sequences. To investigate the relationship between transcription and recombination, transcription promoted by HOT1 was directly examined. These studies demonstrated that transcription starts at the RNA polymerase I initiation site in HOT1 and proceeds through the chromosomal sequences in which recombination is enhanced. Linker insertion mutations in HOT1 were generated and assayed for recombination stimulation and for promoter function; this analysis demonstrated that the same sequences are required for both activities. These results indicate that the ability of HOT1 to enhance recombination is related to, and most likely dependent on, its ability to promote transcription.
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Fleuren, Tobias, Ansgar Thiel, and Annika Frahsa. "Identification of Network Promoters in a Regional and Intersectoral Health Promotion Network: A Qualitative Social Network Analysis in Southern Germany." International Journal of Environmental Research and Public Health 18, no. 16 (August 7, 2021): 8372. http://dx.doi.org/10.3390/ijerph18168372.
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Health in all policies is a key approach to promote health and calls for cooperation between diverse levels of government and different sectors. In this paper, we analyze how a network called ‘Healthy Region Plus’ in Southern Germany addresses intersectoral cooperation at city and county levels. We aim to analyze the different roles of actors involved in the network based on the promoter model. We conducted two socio-material network mappings based on the Net-map approach by Schiffer and Hauck. The analysis followed three steps: data visualization, descriptive analysis of network properties, and interpretation of findings. Our findings reveal a complex intersectoral cooperation structure, with county and city level clusters, with network members who act as diverse power, expert, process, or relationship promoters. We also identified certain relevant sectors not to be part of the network. We discuss that the success of the network depends on the members’ active participation in and their outreach beyond the existing network, between city and county levels, and across sectors to promote health and build health-promoting structures in the region.
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Debeljak, M., P. Frajman, T. Lenasi, M. Narat, A. Baldi, and P. Dovc. "Functional analysis of the bovine beta- and kappa casein gene promoters using homologous mammary gland derived cell line." Archives Animal Breeding 48, no. 4 (October 10, 2005): 334–45. http://dx.doi.org/10.5194/aab-48-334-2005.
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Abstract. Bovine casein gene cluster belongs to the best studied regions of the bovine genome. However, molecular basis of the regulation of casein gene expression is still of great interest for the advancement of milk production. Identification of crucial regulatory regions governing casein gene expression would provide valuable information for marker assisted selection in dairy cattle. In our study we performed comparative analysis of the bovine beta- and kappa casein gene promoter sequences with the regulatory sequences from some other species. In addition, we used homologous mammary gland derived cell culture and luciferase reporter gene system to confirm the functionality of the proximal beta and kappa casein promoters. The longer kappa casein promoter (2064 bp) showed the highest expression level, followed by the short kappa casein promoter (925 bp) and beta casein promoter (1692 bp). Here we demonstrate the suitability of the bovine mammary gland derived cell line BME UV1 for transient gene expression under transcriptional control of the bovine casein gene promoters and compare functionality of different fragments of bovine beta- and kappa casein gene promoters using homologous in vitro system.