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Lee MY, Haam CE, Mun J, Lim G, Lee BH, Oh KS. Development of a FOXM1-DBD Binding Assay for High-Throughput Screening Using TR-FRET Assay. Biol Pharm Bull 2021; 44:1484-1491. [PMID: 34602556 DOI: 10.1248/bpb.b21-00322] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Electrophoretic mobility shift assay (EMSA) technology has been widely employed for the analysis of transcription factors such as Forkhead box protein M1 (FOXM1). However, the application of high-throughput screening (HTS) in performing, such analyses are limited as it uses time consuming electrophoresis procedure and radioisotopes. In this study, we developed a FOXM1-DNA binding domain (DBD) binding assay based on time-resolved fluorescence energy transfer (TR-FRET) that enables HTS for the inhibitors of FOXM1-DNA interaction. This assay was robust, highly reproducible and could be easily miniaturized into 384-well plate format. The signal-to-background (S/B) ratio and Z' factor were calculated as 7.46 and 0.74, respectively, via a series of optimization of the assay conditions. A pilot library screening of 1019 natural compounds was performed using the FOXM1-DBD binding assay. Five hit compounds, namely, AC1LXM, BRN5, gangaleoidin, leoidin, and roemerine were identified as the inhibitors of FOXM1. In a cell viability assay, it was demonstrated that cell proliferation of FOXM1 overexpressed cell lines was suppressed in cell lines such as MDA-MB-231 and MCF-7 by five hit compounds. These results indicate that developed FOXM1-DBD binding assay can be applied to highly efficiency HTS of compound libraries.
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Affiliation(s)
- Mi Young Lee
- Data Convergence Drug Research Center, Korea Research Institute of Chemical Technology
| | - Chae Eun Haam
- Data Convergence Drug Research Center, Korea Research Institute of Chemical Technology.,Graduate School of New Drug Discovery and Development, Chungnam National University
| | - Jihye Mun
- Data Convergence Drug Research Center, Korea Research Institute of Chemical Technology
| | - Gyutae Lim
- Data Convergence Drug Research Center, Korea Research Institute of Chemical Technology
| | - Byung Ho Lee
- Data Convergence Drug Research Center, Korea Research Institute of Chemical Technology.,Graduate School of New Drug Discovery and Development, Chungnam National University
| | - Kwang-Seok Oh
- Data Convergence Drug Research Center, Korea Research Institute of Chemical Technology.,Department of Medicinal and Pharmaceutical Chemistry, University of Science and Technology
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Nargund AM, Fiorese CJ, Pellegrino MW, Deng P, Haynes CM. Mitochondrial and nuclear accumulation of the transcription factor ATFS-1 promotes OXPHOS recovery during the UPR(mt). Mol Cell 2015; 58:123-33. [PMID: 25773600 DOI: 10.1016/j.molcel.2015.02.008] [Citation(s) in RCA: 300] [Impact Index Per Article: 33.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2014] [Revised: 11/11/2014] [Accepted: 02/03/2015] [Indexed: 12/29/2022]
Abstract
Mitochondrial diseases and aging are associated with defects in the oxidative phosphorylation machinery (OXPHOS), which are the only complexes composed of proteins encoded by separate genomes. To better understand genome coordination and OXPHOS recovery during mitochondrial dysfunction, we examined ATFS-1, a transcription factor that regulates mitochondria-to-nuclear communication during the mitochondrial UPR, via ChIP-sequencing. Surprisingly, in addition to regulating mitochondrial chaperone, OXPHOS complex assembly factor, and glycolysis genes, ATFS-1 bound directly to OXPHOS gene promoters in both the nuclear and mitochondrial genomes. Interestingly, atfs-1 was required to limit the accumulation of OXPHOS transcripts during mitochondrial stress, which required accumulation of ATFS-1 in the nucleus and mitochondria. Because balanced ATFS-1 accumulation promoted OXPHOS complex assembly and function, our data suggest that ATFS-1 stimulates respiratory recovery by fine-tuning OXPHOS expression to match the capacity of the suboptimal protein-folding environment in stressed mitochondria, while simultaneously increasing proteostasis capacity.
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Affiliation(s)
- Amrita M Nargund
- Cell Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Christopher J Fiorese
- Cell Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; BCMB Allied Program, Weill Cornell Medical College, New York, NY 10065, USA
| | - Mark W Pellegrino
- Cell Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Pan Deng
- Cell Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; BCMB Allied Program, Weill Cornell Medical College, New York, NY 10065, USA
| | - Cole M Haynes
- Cell Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; BCMB Allied Program, Weill Cornell Medical College, New York, NY 10065, USA.
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Deletion analysis of the catalase-encoding gene (catB) promoter from Aspergillus oryzae. Biosci Biotechnol Biochem 2008; 72:48-53. [PMID: 18175923 DOI: 10.1271/bbb.70321] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The catalase-encoding gene (catB) is expressed strongly in Aspergillus oryzae. To identify the transcription regulatory elements involved in strong expression, we did promoter deletion analysis using beta-glucuronidase (GUS) as a reporter and an electrophoretic gel mobility shift assay (EMSA) systematically. The deletion 200-bp sequence from -1,000 to -800 in the 1,400-bp catB promoter caused a drastic decrease in GUS activity. In addition, EMSA implicated a 45-bp element from -1,000 to -956 containing cis-elements. According to detailed promoter deletion analysis, a region from -1,000 to -975, which contains putative heat shock element (HSE) and the CCAAT-box, was involved in strong expression.
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Ellis T, Evans DA, Martin CRH, Hartley JA. A 96-well DNase I footprinting screen for drug-DNA interactions. Nucleic Acids Res 2007; 35:e89. [PMID: 17586817 PMCID: PMC1919508 DOI: 10.1093/nar/gkm467] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
The established protocol for DNase I footprinting has been modified to allow multiple parallel reactions to be rapidly performed in 96-well microtitre plates. By scrutinizing every aspect of the traditional method and making appropriate modifications it has been possible to considerably reduce the time, risk of sample loss and complexity of footprinting, whilst dramatically increasing the yield of data (30-fold). A semi-automated analysis system has also been developed to present footprinting data as an estimate of the binding affinity of each tested compound to any base pair in the assessed DNA sequence, giving an intuitive ‘one compound–one line’ scheme. Here, we demonstrate the screening capabilities of the 96-well assay and the subsequent data analysis using a series of six pyrrolobenzodiazepine-polypyrrole compounds and human Topoisomerase II alpha promoter DNA. The dramatic increase in throughput, quantified data and decreased handling time allow, for the first time, DNase I footprinting to be used as a screening tool to assess DNA-binding agents.
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Affiliation(s)
- Tom Ellis
- Spirogen Ltd, London Bioscience Innovation Centre, 2 Royal College Street, London, NW1 0NH and Cancer Research UK Drug-DNA Interactions Research Group, Department of Oncology, University College London, 91 Riding House Street, London W1W 7BS, UK
| | - David A. Evans
- Spirogen Ltd, London Bioscience Innovation Centre, 2 Royal College Street, London, NW1 0NH and Cancer Research UK Drug-DNA Interactions Research Group, Department of Oncology, University College London, 91 Riding House Street, London W1W 7BS, UK
| | - Christopher R. H. Martin
- Spirogen Ltd, London Bioscience Innovation Centre, 2 Royal College Street, London, NW1 0NH and Cancer Research UK Drug-DNA Interactions Research Group, Department of Oncology, University College London, 91 Riding House Street, London W1W 7BS, UK
| | - John A. Hartley
- Spirogen Ltd, London Bioscience Innovation Centre, 2 Royal College Street, London, NW1 0NH and Cancer Research UK Drug-DNA Interactions Research Group, Department of Oncology, University College London, 91 Riding House Street, London W1W 7BS, UK
- *To whom correspondence should be addressed. +44 (0)20 7679 9326+44 (0)20 7436 2956
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Moriyama T, Mitsuyama H, Yano E, Ohba M, Kitta K, Kawamoto SI, Akiyama H, Urisu A, Takahashi K, Hajika M, Ogawa T, Kawamura Y. Detection of Food Allergens Using Near-infrared Fluorescent Probes. J JPN SOC FOOD SCI 2007. [DOI: 10.3136/nskkk.54.468] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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Hisada H, Sano M, Ishida H, Hata Y, Abe Y, Machida M. Deletion analysis of the superoxide dismutase (sodM) promoter from Aspergillus oryzae. Appl Microbiol Biotechnol 2006; 72:1048-53. [PMID: 16547700 DOI: 10.1007/s00253-006-0388-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2006] [Revised: 02/16/2006] [Accepted: 02/18/2006] [Indexed: 11/28/2022]
Abstract
The manganese superoxide dismutase gene (sodM) is very highly expressed in Aspergillus oryzae. To elucidate the basis for this high-level expression, deletion analysis of the promoter was undertaken using beta-glucuronidase (GUS) as a reporter. Deletion of a 63-bp sequence from -200 to -138 in the 1,038-bp sodM promoter caused a drastic decrease in GUS activity. In addition, an electrophoretic gel mobility shift assay (EMSA) implicated a 30-bp element from -209 to -178 containing cis-element(s) in the high-level expression. The results of fine structure deletion analysis of this region were consistent with the EMSA results. To confirm these findings, we constructed enhanced sodM promoters by incorporating tandem repeats of this region, which resulted in an approximate twofold increase in expression relative to the native sodM promoter.
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Affiliation(s)
- Hiromoto Hisada
- Research Institute, Gekkeikan Sake Co. Ltd. 101 Shimotoba-koyanagi-cho, Fushimi-ku, Kyoto, 612-8361, Japan.
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Genomics of Economically Significant Aspergillus and Fusarium Species. ACTA ACUST UNITED AC 2004. [DOI: 10.1016/s1874-5334(04)80013-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/21/2023]
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Affiliation(s)
- Masayuki Machida
- Research Center for Glycoscience, National Institute of Advanced Industrial Science and Technology (AIST), Central 6, 1-1, Higashi, Tsukuba, Ibaraki, 305-8566, Japan
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Amirimani B, Ning B, Deitz AC, Weber BL, Kadlubar FF, Rebbeck TR. Increased transcriptional activity of the CYP3A4*1B promoter variant. ENVIRONMENTAL AND MOLECULAR MUTAGENESIS 2003; 42:299-305. [PMID: 14673875 DOI: 10.1002/em.10199] [Citation(s) in RCA: 130] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Numerous single nucleotide polymorphisms (SNPs) have been identified in the human genome, yet the functional significance of most is unknown. CYP3A4 is a key enzyme in the metabolism of numerous compounds. An A-->G substitution 290 bp upstream of the CYP3A4 transcription start site (CYP3A4*1B) has been associated with cancer phenotypes, but its phenotypic effects are unclear. To investigate the functional significance of CYP3A4*1B, we generated two luciferase reporter constructs: 1-kb (denoted L, long) and 0.5-kb (denoted S, short) promoter fragments containing either the variant (V(L),V(S)) or the wild-type (W(L), W(S)) sequences. We evaluated the effect of the variant sequence in the HepG2 and MCF-7 cell lines, and in primary human hepatocytes from three donors. Reporter constructs with the variant sequence had 1.2- to 1.9-fold higher luciferase activity than constructs with wild-type sequence in the cell lines (P < 0.0001) and hepatocytes (P = 0.021, P = 0.027, P = 0.061). The ratio of transcriptional activity for V(S):W(S) was similar to the V(L):W(L) ratio in HepG2 cells, but the V(S):W(S) ratio was consistently less than the V(L):W(L) ratio in MCF-7 cells. This suggests that CYP3A4 expression is higher from the variant promoter and that a repressor sequence may exist in the longer constructs. Electrophoretic mobility shift assays demonstrated specific binding of a component of HepG2 nuclear extract to both wild-type and variant promoters with consistently higher binding affinities to the wild-type sequence. This suggests the existence of a transcriptional repressor responsible for the lower CYP3A4*1A activity. Therefore, the phenotypic effects of the variant CYP3A4*1B may be associated with enhanced CYP3A4 expression due to reduced binding of a transcriptional repressor.
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Affiliation(s)
- B Amirimani
- Department of Medicine, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania 19104-6021, USA
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