• Journal of the Korean Magnetic Resonance Society
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• v.17 no.2
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• pp.76-80
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• 2013

The TCP domain is a DNA-binding domain present in plant transcription factors and has a similar structural feature to the bHTH motif of eukaryotic transcription factors. The imino proton exchange study has been performed for the DNA duplex containing the consensus DNA-binding site for the AtTCP11 transcription factor. The first two base pairs in the consensus 5'-GTGGG-3' sequence are relatively very unstable but lead to greater stabilization of the neighboring two G C base pairs. These unique dynamic features of the five base pairs in the consensus DNA sequence might play crucial roles in the effective DNA binding of the AtTCP11 protein.

• Animal cells and systems
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• v.2 no.1
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• pp.117-122
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• 1998

D-raf, a Drosophila homolog of the human c-raf-1, is known as a signal transducer in cell proliferation and differentiation. A previous study found that the D-raf gene expression is regulated by the DNA replication-related element (DRE)/DRE-binding factor (DREF) system. In this study, we found the sequences homologous to transcription factor C/EBP, MyoD, STAT and Myc recognition sites in the D-raf promoter. We have generated various base substitutional mutations in these recognition sites and subsequently examined their effects on D-raf promoter activity through transient CAT assays in Kc cells with reporter plasmids p5'-878DrafCAT carrying the mutations in these binding sites. Through gel mobility shift assay using nuclear extracts of Kc cells, we detected factors binding to these recognition sites. Our results show that transcription factor C/EBP, STAT and Myc binding sites in D-raf promoter region play a positive role in transcriptional regulation of the D-raf gene and the Myo D binding site plays a negative role.

• BMB Reports
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• v.34 no.4
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• pp.305-309
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• 2001

MatR in Rhizobium trifolii is a malonate-responsive transcription factor that regulates the expression of genes, matABC, enabling decarboxylation of malonyl-CoA into acetyl-CoA, synthesis of malonyl-CoA from malonate and CoA, and malonate transport. According to an analysis of the amino acid sequence homology, MatR belongs to the GntR family The proteins of this family have two-domain folds, the N-terminal helix-turn-helix DNA-binding domain and the C-terminal ligand-binding domain. In order to End the malonate binding site and amino acid residues that interact with RNA polymerase, a site-directed mutagenesis was performed. Analysis of the mutant MatR suggests that Arg-160 might be involved in malonate binding, whereas Arg-102 and Arg-174 are critical for the repression activity by interacting with RNA polymerase.

• Journal of the Korean Magnetic Resonance Society
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• v.18 no.2
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• pp.52-57
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• 2014

The TCP domain is a DNA-binding domain present in plant transcription factors and plays important roles in various biological functions. The hydrogen exchange rate constants of the imino protons were determined for the three DNA duplexes containing the DNA-binding sites for the TCP11, TCP15, and TCP20 transcription factors using NMR spectroscopy. The M11 duplex displays unique hydrogen exchange property of the five base pairs in the first binding site (5'-GTGGG-3'). However, the M15 and M20 duplexes lead to clear changes in thermal stabilities of these five base pairs. The unique dynamic features of the five base pairs in the first binding site might play crucial roles in the sequence-specific DNA binding of the class I TCP transcription factors.

• Journal of Life Science
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• v.13 no.5
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• pp.746-750
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• 2003

Lactose operon contains two CRP binding sites at promoter(CRP1 site) and operator(CRP2 site) regions at lac operon. CRP protein can bind to both sites with the different binding affinity. CRP1 site, major CRP binding site, acts the transcription activation with the fully unknown mechanism by binding of CRP. In this study, the binding affinities of CRP1 site and CRP2 site were measured with the fluorescein-labeled oligomers, which contain CRP1 site and the three different spacing sequences between GTGA and TCAC at CRP2 site. Results showed that CRP:cAMP complex bound to CRP1 site 3 times more strongly than CRP2 site and the base spacing between GTGA and TCAC was not the only factor to affect the binding affinity of CRP to CRP2 site.

• Tuberculosis and Respiratory Diseases
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• v.48 no.6
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• pp.879-886
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• 2000

Background : Thyroid Transcription Factor-1(TTF-1) acts as a tissue specific transcription factor in the regulation of lung specific gene expression and as morphogenic protein during lung organogenesis. Currently, there is very little information on the cis-acting sequences and transcription factors that direct the TTF-1 gene expression. DNAse 1 hypersensitive (DH) sites represent a marker for active or potentially active chromatin and are likely to be especially important in gene regulation, being associated with many DNA sequences that regulate gene expression. It is clear that DH regions correlate with genetic regulatory loci and binding for sequence-specific DNA-binding proteins. Methods : We have used DH site assays to identify putative distal regulatory elements in H441 lung adenocarcinoma cells, which express the TTF-1 gene and HeLa cells. Results : There are four DH sites 5' of the TTF-1 gene. These sites are located at base pair approximately +150, -450, -800, and -1500 from the start of transcription. Conclusion : These data suggest that there may be at least one intragenic site and regulatory region 5' prime to the promotor region.

• BMB Reports
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• v.42 no.12
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• pp.788-793
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• 2009

TLX2 is an orphan homeodomain transcription factor whose expression is mainly associated with tissues derived from neural crest cells. Recently, we have demonstrated that PHOX2A and PHOX2B are able to enhance the neural cell-type specific expression of human TLX2 by binding distally the 5' -flanking region. In the present work, to deepen into the TLX2 transcription regulation, we have focused on the proximal 5'-flanking region of the gene, mapping the transcription start site and identifying a minimal promoter necessary and sufficient for the basal transcription in cell lines from different origin. Site-directed mutagenesis has allowed to demonstrate that the integrity of this sequence is crucial for gene expression, while electrophoretic mobility shift assays and chromatin immunoprecipitation experiments have revealed that such an activity is dependent on the binding of a PBX factor. Consistent with these findings, such a basal promoter activity has resulted to be enhanced by the previously reported PHOX2-responding sequence.

• Journal of the Korean Magnetic Resonance Society
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• v.24 no.4
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• pp.117-122
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• 2020

Transcription factors are proteins that bind specific sites or elements in regulatory regions of DNA, known as promoters or enhancers, where they control the transcription or expression of target genes. MEIS1 protein is a DNA-binding domain present in human transcription factors and plays important roles in various biological functions. The hydrogen exchange rate constants of the imino protons were determined for the wild-type containing the consensus DNA-binding site for the MEIS1 and those of the mutant DNA duplexes using NMR spectroscopy. The G2A-, A3G- and C4T-mutant DNA duplexes lead to clear changes in thermal stabilities of these four consensus base pairs. These unique dynamic features of the four base pairs in the consensus 5'-TGAC-3' sequence might play crucial roles in the effective DNA binding of the MEIS1 protein.

• Journal of KIISE:Software and Applications
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• v.30 no.5_6
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• pp.487-496
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• 2003

The promoter that plays a very important role in gene expression as a signal part has various binding sites for transcription factors. These binding sites are located on various parts in promoter region and have highly conserved consensus sequence patterns. This paper presents a new method for the consensus pattern search in promoter regions using genetic algorithm, which adopts the assumption of N-occurrence-per-dataset model of MEME algorithm and employs the advantage of Wataru method in determining the pattern length. Our method will be employed by genome researchers who try to predict the promoter region on anonymous DNA sequence and to find out the binding site for a specific transcription factor.

• Asian-Australasian Journal of Animal Sciences
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• v.31 no.3
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• pp.449-456
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• 2018

Objective: Nanog, a homeodomain protein, has been investigated in humans and mice using embryonic stem cells (ESCs). Because of the limited availability of ESCs, few studies have reported the function and role of Nanog in porcine ESCs. Therefore, in this study, we investigated the location of the porcine Nanog chromosome and its basal promoter activity, which might have potential applications in development of ESCs specific marker as well as understanding its operating systems in the porcine. Methods: To characterize the porcine Nanog promoter, the 5'-flanking region of Nanog was isolated from cells of mini-pig ears. BLAST database search showed that there are two porcine Nanog genomic loci, chromosome 1 and 5, both of which contain an exon with a start codon. Deletion mutants from the 5'-flanking region of both loci were measured using the Dual-Luciferase Reporter Assay System, and a fluorescence marker, green fluorescence protein. Results: Promoter activity was detected in the sequences of chromosome 5, but not in those of chromosome 1. We identified the sequences from -99 to +194 that possessed promoter activity and contained transcription factor binding sites from deletion fragment analysis. Among the transcription factor binding sites, a Sp1 was found to play a crucial role in basal promoter activity, and point mutation of this site abolished its activity, confirming its role in promoter activity. Furthermore, gel shift analysis and chromatin immunoprecipitation analysis confirmed that Sp1 transcription factor binds to the Sp1 binding site in the porcine Nanog promoter. Taken together, these results show that Sp1 transcription factor is an essential element for porcine Nanog basal activity the same as in human and mouse. Conclusion: We showed that the porcine Nanog gene is located on porcine chromosome 5 and its basal transcriptional activity is controlled by Sp1 transcription factor.