scholarly journals A 37-base pair element in the far upstream spacer region can enhance transcription of rat rDNA in vitro and can bind to the core promoter-binding factor(s)

1989 ◽  
Vol 264 (1) ◽  
pp. 220-224
Author(s):  
L C Garg ◽  
A Dixit ◽  
S T Jacob
Keyword(s):  
Base Pair ◽  
Core Promoter ◽  
The Core ◽  
Binding Factor

scholarly journals Investigation of the Wilson gene ATP7B transcriptional start site and the effect of core promoter alterations

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Clemens Höflich ◽  
Angela Brieger ◽  
Stefan Zeuzem ◽  
Guido Plotz
Keyword(s):  
Wilson Disease ◽  
Transcription Initiation ◽  
Transcriptional Activity ◽  
Core Promoter ◽  
Transcriptional Start Site ◽  
Copper Metabolism ◽  
Biologically Relevant ◽  
The Core ◽  
Translational Start

AbstractPathogenic genetic variants in the ATP7B gene cause Wilson disease, a recessive disorder of copper metabolism showing a significant variability in clinical phenotype. Promoter mutations have been rarely reported, and controversial data exist on the site of transcription initiation (the core promoter). We quantitatively investigated transcription initiation and found it to be located in immediate proximity of the translational start. The effects human single-nucleotide alterations of conserved bases in the core promoter on transcriptional activity were moderate, explaining why clearly pathogenic mutations within the core promoter have not been reported. Furthermore, the core promoter contains two frequent polymorphisms (rs148013251 and rs2277448) that could contribute to phenotypical variability in Wilson disease patients with incompletely inactivating mutations. However, neither polymorphism significantly modulated ATP7B expression in vitro, nor were copper household parameters in healthy probands affected. In summary, the investigations allowed to determine the biologically relevant site of ATP7B transcription initiation and demonstrated that genetic variations in this site, although being the focus of transcriptional activity, do not contribute significantly to Wilson disease pathogenesis.

scholarly journals GGeneration of an efficient artificial promoter of bovine skeletal muscle alpha-actin gene (ACTA1) through addition of cis-acting element

2015 ◽  
Vol 20 (1) ◽  
Author(s):  
Qian Hu ◽  
Huili Tong ◽  
Dandan Zhao ◽  
Yunkao Cao ◽  
Weiwei Zhang ◽  
...  
Keyword(s):  
Skeletal Muscle ◽  
Core Promoter ◽  
Genetically Engineered ◽  
Actin Gene ◽  
Base Pairs ◽  
Cis Acting ◽  
The Core ◽  
Binding Factor ◽  
Bovine Skeletal Muscle ◽  
Alpha Actin

AbstractThe promoter of skeletal muscle α-actin gene (ACTA1) is highly muscle specific. The core of the bovine ACTA1 promoter extends from +29 to −233, about 262 base pairs (bp), which is sufficient to activate transcription in bovine muscle satellite cells. In this study, analysis by PCR site-specific mutagenesis showed that the cis-acting element SRE (serum response element binding factor) was processed as a transcriptional activator. In order to enhance the bovine ACTA1 promoter’s activity, we used a strategy to modify it. We cloned a fragment containing three SREs from the promoter of ACTA1, and then one or two clones were linked upstream of the core promoter (262 bp) of ACTA1. One and two clones increased the activity of the ACTA1 promoter 3-fold and 10-fold, respectively, and maintained muscle tissue specificity. The modified promoter with two clones could increase the level of ACTA1 mRNA and protein 4-fold and 1.1-fold, respectively. Immunofluorescence results showed that green fluorescence of ACTA1 increased. Additionally, the number of total muscle microfilaments increased. These genetically engineered promoters might be useful for regulating gene expression in muscle cells and improving muscle mass in livestock.

Identification of the crossover site during FLP-mediated recombination in the Saccharomyces cerevisiae plasmid 2 microns circle

1986 ◽  
Vol 6 (10) ◽  
pp. 3357-3367
Author(s):  
M McLeod ◽  
S Craft ◽  
J R Broach
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Base Pair ◽  
Low Frequency ◽  
Strand Exchange ◽  
Crossover Point ◽  
Core Domain ◽  
The Core ◽  
Crossover Site

The FLP protein of the Saccharomyces cerevisiae plasmid 2 microns circle catalyzes site-specific recombination between two repeated segments present on the plasmid. In this paper we present results of experiments we performed to define more precisely the features of the FLP recognition target site, which we propose to designate FRT, and to determine the actual recombination crossover point in vivo. We found that essential sequences for the recombination event are limited to an 8-base-pair core sequence and two 13-base-pair repeated units immediately flanking it. This is the region identified as the FLP binding site in vitro and at which FLP protein promotes specific single-strand cleavages (B. J. Andrews, G. A. Proteau, L. G. Beatty, and P. D. Sadowski, Cell 40:795-803, 1985; J. F. Senecoff, R. C. Bruckner, and M. M. Cox, Proc. Natl. Acad. Sci. USA 82:7270-7274, 1985). Mutations within the core domain can be suppressed by the presence of the identical mutation in the chromatid with which it recombines. However, mutations outside the core are not similarly suppressed. We found that strand exchange during FLP recombination occurs most of the time within the core region, proceeding through a heteroduplex intermediate. Finally, we found that most FLP-mediated events are reciprocal exchanges and that FLP-catalyzed gene conversions occur at low frequency. The low level of gene conversion associated with FLP recombination suggests that it proceeds by a breakage-joining reaction and that the two events are concerted.

scholarly journals Requirements for Brome Mosaic Virus Subgenomic RNA Synthesis In Vivo and Replicase-Core Promoter Interactions In Vitro

2004 ◽  
Vol 78 (12) ◽  
pp. 6091-6101 ◽  
Author(s):  
K. Sivakumaran ◽  
Seung-Kook Choi ◽  
Masarapu Hema ◽  
C. Cheng Kao
Keyword(s):  
Mosaic Virus ◽  
Rna Synthesis ◽  
Core Promoter ◽  
Brome Mosaic Virus ◽  
Wild Type ◽  
Subgenomic Rna ◽  
The Core ◽  
Rna Hairpin

ABSTRACT Based solely on in vitro results, two contrasting models have been proposed for the recognition of the brome mosaic virus (BMV) subgenomic core promoter by the replicase. The first posits that the replicase recognizes at least four key nucleotides in the core promoter, followed by an induced fit, wherein some of the nucleotides base pair prior to the initiation of RNA synthesis (S. Adkins and C. C. Kao, Virology 252:1-8, 1998). The second model posits that a short RNA hairpin in the core promoter serves as a landing pad for the replicase and that at least some of the key nucleotides help form a stable hairpin (P. C. J. Haasnoot, F. Brederode, R. C. L. Olsthoorn, and J. Bol, RNA 6:708-716, 2000; P. C. J. Haasnoot, R. C. L. Olsthoorn, and J. Bol, RNA 8:110-122, 2002). We used transfected barley protoplasts to examine the recognition of the subgenomic core promoter by the BMV replicase. Key nucleotides required for subgenomic initiation in vitro were found to be important for RNA4 levels in protoplasts. In addition, additional residues not required in vitro and the formation of an RNA hairpin within the core promoter were correlated with wild-type RNA4 levels in cells. Using a template competition assay, the core promoter of ca. 20 nucleotides was found to be sufficient for replicase binding. Mutations of the key residues in the core promoter reduced replicase binding, but deletions that disrupt the predicted base pairing in the proposed stem retained binding at wild-type levels. Together, these results indicate that key nucleotides in the BMV subgenomic core promoter direct replicase recognition but that the formation of a stem-loop is required at a step after binding. Additional functional characterization of the subgenomic core promoter was performed. A portion of the promoter for BMV minus-strand RNA synthesis could substitute for the subgenomic core promoter in transfected cells. The comparable sequence from Cowpea Chlorotic Mottle Virus (CCMV) could also substitute for the BMV subgenomic core promoter. However, nucleotides in the CCMV core required for RNA synthesis are not identical to those in BMV, suggesting that the subgenomic core promoter can induce the BMV replicase in interactions needed for subgenomic RNA transcription in vivo.

scholarly journals Selective Promoter Recognition by Chlamydial σ28 Holoenzyme

2006 ◽  
Vol 188 (21) ◽  
pp. 7364-7377 ◽  
Author(s):  
Li Shen ◽  
Xiaogeng Feng ◽  
Yuan Yuan ◽  
Xudong Luo ◽  
Thomas P. Hatch ◽  
...  
Keyword(s):  
Core Promoter ◽  
Sigma Factors ◽  
Promoter Sequences ◽  
E Coli ◽  
The Core ◽  
Recognition Specificity ◽  
Promoter Recognition ◽  
Transcription In Vitro

ABSTRACT The σ transcription factor confers the promoter recognition specificity of RNA polymerase (RNAP) in eubacteria. Chlamydia trachomatis has three known sigma factors, σ66, σ54, and σ28. We developed two methods to facilitate the characterization of promoter sequences recognized by C. trachomatis σ28 (σ28 Ct). One involved the arabinose-induced expression of plasmid-encoded σ28 Ct in a strain of Escherichia coli defective in the σ28 structural gene, fliA. The second was an analysis of transcription in vitro with a hybrid holoenzyme reconstituted with E. coli RNAP core and recombinant σ28 Ct. These approaches were used to investigate the interactions of σ28 Ct with the σ28 Ct-dependent hctB promoter and selected E. coli σ28 (σ28 Ec)-dependent promoters, in parallel, compared with the promoter recognition properties of σ28 EC. Our results indicate that RNAP containing σ28 Ct has at least three characteristics: (i) it is capable of recognizing some but not all σ28 EC-dependent promoters; (ii) it can distinguish different promoter structures, preferentially activating promoters with upstream AT-rich sequences; and (iii) it possesses a greater flexibility than σ28 EC in recognizing variants with different spacing lengths separating the −35 and −10 elements of the core promoter.

scholarly journals The Transcription Factor CCAAT-binding Factor CBF/NF-Y and Two Repressors Regulate the Core Promoter of the Human Pro-α3(V) Collagen Gene (COL5A3)

2004 ◽  
Vol 279 (45) ◽  
pp. 46373-46383 ◽  
Author(s):  
Hitoshi Nagato ◽  
Noritaka Matsuo ◽  
Hideaki Sumiyoshi ◽  
Keiko Sakata-Takatani ◽  
Masaru Nasu ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Core Promoter ◽  
Collagen Gene ◽  
The Core ◽  
Binding Factor

scholarly journals SMAD4 Feedback Activates The Canonical TGF-β Family Signaling Pathways

2021 ◽  
Author(s):  
Xing Du ◽  
Qiqi Li ◽  
Liu Yang ◽  
Qifa Li
Keyword(s):  
Signaling Pathways ◽  
Core Promoter ◽  
Genetic Regulation ◽  
Feedback Regulation ◽  
Bmp Signaling ◽  
The Core ◽  
Porcine Granulosa Cells ◽  
Health And Disease ◽  
And Function

Abstract Background: TGF-β family signaling pathways, including TGF-β and BMP signaling pathways, are widely involved in the regulation of health and disease, which are also regulated by multiple validated mechanisms, such as genetic regulation, epigenetic regulation, and feedback regulation. The objective of this research is to investigate the molecular mechanism and function mode of SMAD4 directly feedback regulation of TGF-β family signaling pathways in porcine granulosa cells (GC).Results: The transcriptomic alteration of porcine GCs induced by SMAD4 silencing was re-analyzed with the background of Sus scrofa RefSeq 11.1 (Sscrofa 11.1). A total of 986 differentially expressed mRNAs (DEmRNAs) were identified, including 467 down-regulated and 519 up-regulated genes. Functional assessment showed the impacts of DEmRNAs on the regulation of states and function of GCs, and the oocyte development. As the upstream receptors of SMAD4, ACVR1B, BMPR2, and TGFBR2 were selected from down-regulated DEmRNAs for further research. In vitro, qRT-PCR and western blotting were performed and confirmed that SMAD4 significantly induced the expression of ACVR1B, BMPR2, and TGFBR2 in porcine GCs. Besides, RACE and luciferase activity assays were carried out to identified the core promoter of porcine ACVR1B, BMPR2, and TGFBR2. Results from ChIP assays showed that SMAD4 directly binds to the SMAD4 binding elements (SBEs) within the core promoter of its upstream receptors by acting as a transcription factor. Furthermore, c-JUN, CREB1, and SP1 were identified as SMAD4-interacted co-activators by IP assays and inhibition of which could dramatically suppress the expression of porcine ACVR1B, BMPR2, and TGFBR2 that induced by SMAD4 over-expression. Furthermore, three different interaction modes between SMAD4 and co-activators were identified by reciprocal ChIP assays.Conclusions: Take together, our findings revealed a novel feedback regulatory mechanism of TGF-β family signaling pathways in porcine GCs, and demonstrated for the first time that SMAD4, the only Co-SMAD, directly feedback activates the transcription of canonical TGF-β family signaling pathway receptors by interacting with three co-activators in different modes, which improves and expands the regulatory network, especially the feedback regulation modes of TGF-β family signaling pathways in the ovary.

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