• Biomolecules & Therapeutics
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• v.29 no.6
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• pp.667-677
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• 2021

The elevated expression of the hyaluronan-mediated motility receptor (HMMR) is known to be highly associated with tumor progression in prostate cancer, but the molecular mechanisms underlying the regulation of HMMR expression remain unclear. Here, we report that mammalian target of rapamycin (mTOR) is a key regulator of HMMR expression, for which its kinase activity is required. Pharmacological inhibitors of mTOR, such as rapamycin and Torin2, markedly suppressed the mRNA level as well as the protein level of HMMR in LNCaP and PC-3 cells. Our data demonstrate that such regulation occurs at the transcription level. HMMR promoter reporter assays revealed that the transcription factor SRF is responsible for the mTOR-mediated transcriptional regulation of HMMR gene. Consistently, the suppression of HMMR expression by Torin2 was noticeably reversed by the overexpression of SRF. Moreover, our findings suggest that the SRF binding sites responsible for the transcriptional regulation of HMMR through the mTOR-SRF axis are located in HMMR promoter sequences carrying the first intron, downstream of the translational start site. Furthermore, the upregulation of HMMR by DHT was abolished by stimulation with rapamycin, prior to DHT treatment, suggesting that mTOR activity is required for the induction of HMMR expression by androgen. Collectively, our study provides new mechanistic insights into the role of mTOR/SRF/AR signaling in HMMR regulation in prostate cancer cells.

• Mycobiology
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• v.28 no.4
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• pp.171-176
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• 2000

We have cloned a ${\alpha}-COP$ homolog, ancop, from Aspergillus nidulans by colony hybridization of chromosome specific library using ${\alpha}-COP$ homologous fragment as a probe. The probe DNA was amplified with degenerated primers designed by comparison of conserved region of the amino acid sequences of Saccharomyces cerevisiae ${\alpha}-COP$, Homo sapiens HEP-COP, and Drosophila melanogaster ${\alpha}-COP$. Full length cDNA clone was also amplified by RT-PCR. Comparison of genomic DNA sequence with cDNA sequence obtained by RT-PCR revealed 7 introns. Amino acid sequence similarity search of the anCop with other ${\alpha}-COPs$ gave an overall identity of 52% with S. cerevisiae, 47% with human and bovine, 45% with Drosophila and Arabidopsis. In upstream region from the transcription start site, a putative TATA and CAAT motif were also identified.

• BMB Reports
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• v.44 no.2
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• pp.113-117
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• 2011

Previous studies suggest that EphA7 plays a critical role in neural tube closure or cortical progenitor apoptosis. In this report, enhancer trap assay was used to modify various EphA7 BAC clones and screen a large genomic region spanning 570 kb downstream of the EphA7 gene. We found that the dorsal midline-specific EphA7 enhancer resides on the 457D20 EphA7 BAC clone and is localized to a 35 kb genomic region in between +345.7 kb to +379.8 kb downstream of the EphA7 transcription start site. Identification of the EphA7 BAC clone containing a long-range dorsal midline enhancer may constitute a useful tool for investigating the biological functions of EphA7 in vivo.

• Journal of Photoscience
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• v.3 no.2
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• pp.85-90
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• 1996

The binding ability of leaf nuclear extracts to the lighbresponsive elements (LREs) of cab promoters of Arabidopsis thaliana has been investigated. The cab promoters were fragmented with restr ction endonucleases into LRE that were identified by Mitra et al. [Plant Mol. Biol. 12, 169179 ( 1989)] and other small fragments. After end labeling with Klenow fragment, the fragments were assayed for binding with the leaf nuclear proteins that were prepared by solubilizing the purified nuclei with 0.5 M ammonium sulfate. The binding ability was assayed by mobility shift assay. To perform successful mobility shift assay, several factors affecting the interaction of protein with DNA were optimized before performing the assay. The LREs had several retardation bands. However, the other promoter fragments from the transcription start site to the far upstream region of the promoters had also retardation bands. No particular relationships could be found between the retardation band distributions and the loci of LRE. It is likely that the light-regulation of cab gene expression may be controlled by the multiple interactions of the regulatory protein factors with DNA motifs.

• Genomics & Informatics
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• v.9 no.4
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• pp.194-196
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• 2011

Promoter prediction is a very important problem and is closely related to the main problems of bioinformatics such as the construction of gene regulatory networks and gene function annotation. In this context, we developed an integrated promoter prediction program using hybrid methods, PromoterWizard, which can be employed to detect the core promoter region and the transcription start site (TSS) in vertebrate genomic DNA sequences, an issue of obvious importance for genome annotation efforts. PromoterWizard consists of three main modules and two auxiliary modules. The three main modules include CDRM (Composite Dependency Reflecting Model) module, SVM (Support Vector Machine) module, and ICM (Interpolated Context Model) module. The two auxiliary modules are CpG Island Detector and GCPlot that may contribute to improving the predictive accuracy of the three main modules and facilitating human curator to decide on the final annotation.

• Proceedings of the Korean Information Science Society Conference
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• 2003.10b
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• pp.769-771
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• 2003

PromSearch는 DNA 염기서열 상에서 프로모터의 위치를 예측하는 프로그램이다. 다루는 대상은 인간 DNA의 프로모터이며, 프로모터의 TSS(transcription start site, 전사시작지점)를 예측하는 것을 목표로 한다. 프로모터 영역을 세분하여 각 영역에 대한 프로파일을 PWM(position weight matrix)을 이용해 작성하며, 임의의 염기서열이 입력으로 주어지면 세분한 영역의 점수를 신경망을 이용해 통합하여 프로모터 여부와 TSS의 위치를 결정한다. 프로모터 영역의 분할은 코어 프로모터의 구성 요소인 TATA-box와 Inr, DPE(downstream promoter element), 그리고 코어 프로모터의 위쪽으로 150bp 크기의 영역 등으로 4분할하였다. Fickett의 데이터를 이용한 평가 결과 sensitivity 43%, specificity 88fp(1/376bp)의 성능을 보였다.

• Molecules and Cells
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• v.42 no.2
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• pp.123-134
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• 2019

Lysophosphatidic acid (LPA) is an endogenous lysophospholipid with signaling properties outside of the cell and it signals through specific G protein-coupled receptors, known as $LPA_{1-6}$. For one of its receptors, $LPA_1$ (gene name Lpar1), details on the cis-acting elements for transcriptional control have not been defined. Using 5'RACE analysis, we report the identification of an alternative transcription start site of mouse Lpar1 and characterize approximately 3,500 bp of non-coding flanking sequence 5' of mouse Lpar1 gene for promoter activity. Transient transfection of cells derived from mouse neocortical neuroblasts with constructs from the 5' regions of mouse Lpar1 gene revealed the region between -248 to +225 serving as the basal promoter for Lpar1. This region also lacks a TATA box. For the region between -761 to -248, a negative regulatory element affected the basal expression of Lpar1. This region has three E-box sequences and mutagenesis of these E-boxes, followed by transient expression, demonstrated that two of the E-boxes act as negative modulators of Lpar1. One of these E-box sequences bound the HeLa E-box binding protein (HEB), and modulation of HEB levels in the transfected cells regulated the transcription of the reporter gene. Based on our data, we propose that HEB may be required for a proper regulation of Lpar1 expression in the embryonic neocortical neuroblast cells and to affect its function in both normal brain development and disease settings.

• Journal of Life Science
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• v.22 no.9
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• pp.1201-1206
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• 2012

The Crlz1 gene is known to be expressed specifically in the pre-B cell stage during B-cell development. With regards to the specific expression of the pre-B cell stage of the Crlz1 gene, we have previously identified three pre-B cell-specific DNase I hypersensitive sites (HSS), which are named HSS8, 9, and 10, in the upstream vicinity of this gene. In this paper, we report that HSS8 increases further the strong Crlz1 promoter activity driven by HSS9/10 and, therefore, acts as its enhancer. Furthermore, HSS8 has been finely mapped between -1055 and -1159 from the transcription start site of the Crlz1 gene.

• Animal Bioscience
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• v.34 no.2
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• pp.172-184
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• 2021

Objective: Vanin1 (VNN1) is a pantetheinase that can catalyze the hydrolysis of pantetheine to produce pantothenic acid and cysteamine. Our previous studies showed that VNN1 is specifically expressed in chicken liver. In this study, we aimed to investigate the roles of peroxisome proliferators activated receptor α (PPARα) and miRNA-181a-5p in regulating VNN1 gene expression in chicken liver. Methods: 5'-RACE was performed to identify the transcription start site of chicken VNN1. JASPAR and TFSEARCH were used to analyze the potential transcription factor binding sites in the promoter region of chicken VNN1 and miRanda was used to search miRNA binding sites in 3' untranslated region (3'UTR) of chicken VNN1. We used a knock-down strategy to manipulate PPARα (or miRNA-181a-5p) expression levels in vitro to further investigate its effect on VNN1 gene transcription. Luciferase reporter assays were used to explore the specific regions of VNN1 targeted by PPARα and miRNA-181a-5p. Results: Sequence analysis of the VNN1 promoter region revealed several transcription factor-binding sites, including hepatocyte nuclear factor 1α (HNF1α), PPARα, and CCAAT/enhancer binding protein α. GW7647 (a specific agonist of PPARα) increased the expression level of VNN1 mRNA in chicken primary hepatocytes, whereas knockdown of PPARα with siRNA increased VNN1 mRNA expression. Moreover, the predicted PPARα-binding site was confirmed to be necessary for PPARα regulation of VNN1 gene expression. In addition, the VNN1 3'UTR contains a sequence that is completely complementary to nucleotides 1 to 7 of miRNA-181a-5p. Overexpression of miR-181a-5p significantly decreased the expression level of VNN1 mRNA. Conclusion: This study demonstrates that PPARα is an important transcriptional activator of VNN1 gene expression and that miRNA-181a-5p acts as a negative regulator of VNN1 expression in chicken hepatocytes.

• Journal of the Korean Association of Oral and Maxillofacial Surgeons
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• v.36 no.6
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• pp.481-489
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• 2010

Introduction: TLR-5, a member of the toll-like receptor (TLR) family, is a element of the type I transmembrane receptors, which are characterized by an intracellular signaling domain homolog to the interleukin-1 receptor. These receptors recognize microbial components, particularly bacterial flagellin. All-trans retinoic acid (atRA, tretinoin), a natural metabolite of vitamin A, acts as a growth and differentiation factor in many tissues, and is also needed for immune functions. In this study, THP-1 human macrophage-monocytes were used to examine the mechanisms by which atRA regulated the expression of TLR-5. Because the molecular mechanism underlying this regulation at the transcriptional level is also unclear, this study examined which putative transcription factors are responsible for TLR-5 expression by atRA in immune cells. Materials and Methods: This study examined whether atRA induces the expression of TLR-5 in THP-1 cells using reverse transcription-polymerase chain reaction (RT-PCR), and which transcription factors are involved in regulating the TLR-5 promoter in RAW264.7 cells using a reporter assay system. Western blot analysis was used to determine which signal pathway is involved in the expression of TLR-5 in atRA-treated THP-1 cells. Results: atRA at a concentration of 10 nM greatly induced the expression of TLR-5 in THP-1 cells. Human TLR-5 promoter contains three Sp-1/GC binding sites around -50 bp and two NF-kB binding sites at -380 bp and -160 bp from the transcriptional start site of the TLR-5 gene. Sp-1/GC is primarily responsible for the constitutive TLR-5 expression, and may also contribute to NF-kB at -160 bp to induce TLR-5 after atRA stimulation in THP-1 cells. The role of NF-kB in TLR-5 expression was further confirmed by inhibitor pyrrolidine dithiocarbamate (PDTC) experiments, which greatly reduced the TLR-5 transcription by 70-80%. Conclusion: atRA induces the expression of the human TLR-5 gene and NF-kB is a critical transcription factor for the atRA-induced expression of TLR-5. Accordingly, it is conceivable that retinoids are required for adequate innate and adaptive immune responses to agents of infectious diseases. atRA and various synthetic retinoids have been used therapeutically in human diseases, such as leukemia and other cancers due to the antiproliferative and apoptosis inducing effects of retinoids. Therefore, understanding the molecular regulatory mechanism of TLR-5 may assist in the design of alternative strategies for the treatment of infectious diseases, leukemia and cancers.