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Song H, He Y, Ma L, Zhou X, Liu X, Qi J, Zhang Q. Characterisation of kisspeptin system genes in an ovoviviparous teleost: Sebastes schlegeli. Gen Comp Endocrinol 2015; 214:114-25. [PMID: 24955882 DOI: 10.1016/j.ygcen.2014.06.010] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/20/2014] [Revised: 06/08/2014] [Accepted: 06/12/2014] [Indexed: 11/27/2022]
Abstract
Kisspeptins are neuropeptides that play important roles in the reproduction and the onset of puberty in vertebrate by activating their receptor, Kissr. In the present study, we first isolated kiss1 and kissr4 genes from an ovoviviparous fish, the black rockfish (Sebastes schlegeli) by homologue cloning. Phylogenetic analysis indicated that the kiss and kissr of S. schlegeli belonged to kiss1 and kissr4 respectively. Quantitative real-time PCR analysis showed that the kissr4 was expressed mainly in the brain and testis, while the kiss1 was expressed predominantly in the heart of both sexes. As for the different gonadal maturation stages the kiss1 showed different expression patterns in different tissues. During the early development stage, expression levels of the ligand and receptor genes showed similar increasing trends. The promoter region of kissr4 contained several putative transcription factor (TF) binding sites which may have the function of regulating kisspeptin system gene expression, providing potential targets for future in-depth investigation. These results together confirmed that the kisspeptin system in S. schlegeli may be involved in reproduction and other activities. Furthermore, our study laid the groundwork for further learning about the evolution and function of kisspeptin system in fish even vertebrate.
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Affiliation(s)
- Huayu Song
- Key Laboratory of Marine Genetics and Breeding, Ministry of Education, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, PR China
| | - Yan He
- Key Laboratory of Marine Genetics and Breeding, Ministry of Education, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, PR China
| | - Liman Ma
- Key Laboratory of Marine Genetics and Breeding, Ministry of Education, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, PR China
| | - Xiaosu Zhou
- Key Laboratory of Marine Genetics and Breeding, Ministry of Education, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, PR China
| | - Xiumei Liu
- Key Laboratory of Marine Genetics and Breeding, Ministry of Education, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, PR China
| | - Jie Qi
- Key Laboratory of Marine Genetics and Breeding, Ministry of Education, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, PR China.
| | - Quanqi Zhang
- Key Laboratory of Marine Genetics and Breeding, Ministry of Education, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, PR China.
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2
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Ishida M, Mitsui T, Izawa M, Arita J. Activation of D2 dopamine receptors inhibits estrogen response element-mediated estrogen receptor transactivation in rat pituitary lactotrophs. Mol Cell Endocrinol 2013; 375:58-67. [PMID: 23701824 DOI: 10.1016/j.mce.2013.05.011] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/07/2013] [Revised: 04/15/2013] [Accepted: 05/10/2013] [Indexed: 11/21/2022]
Abstract
Estrogen and dopamine are major opposing regulators of the endocrine functions of pituitary lactotrophs. Dopamine inhibits estrogen-induced changes in the synthesis and secretion of prolactin, and lactotroph proliferation. We studied the mechanism of the inhibitory effects of dopaminergic stimulation on estrogen-induced functional changes of rat lactotrophs in primary culture. The dopaminergic agonist, bromocriptine (BC), suppressed 17β-estradiol-stimulated lactotroph proliferation, prolactin promoter activity, and mRNA expression of some estrogen-responsive genes. In lactotroph-enriched pituitary cells, BC treatment inhibited the estrogen response element (ERE) DNA sequence-mediated estrogen receptor (ER) transcriptional activity. Using a lactotroph-specific ERE transcriptional assay, we found that BC inhibition of the ERE-mediated ER transcriptional activity partly involved D2 dopamine receptor-mediated, pertussis toxin-sensitive G protein-coupled, cAMP/protein kinase A-dependent signaling. BC treatment had no effect on the cellular concentration of ERα or its phosphorylation status at Ser-118. Similar transcriptional inhibition by BC was also found in GH4ZR7 cells, a D2 dopamine receptor-expressing somatomammotrophic cell line. These results suggest that activation of the D2 dopamine receptors inhibits estrogen-dependent lactotroph functions in part via attenuation of ERE-mediated ER transactivation.
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Affiliation(s)
- Maho Ishida
- Department of Physiology, Interdisciplinary Graduate School of Medicine and Engineering, University of Yamanashi, Yamanashi 409-3898, Japan.
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3
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Hestand MS, van Galen M, Villerius MP, van Ommen GJB, den Dunnen JT, 't Hoen PAC. CORE_TF: a user-friendly interface to identify evolutionary conserved transcription factor binding sites in sets of co-regulated genes. BMC Bioinformatics 2008; 9:495. [PMID: 19036135 PMCID: PMC2613159 DOI: 10.1186/1471-2105-9-495] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2008] [Accepted: 11/26/2008] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The identification of transcription factor binding sites is difficult since they are only a small number of nucleotides in size, resulting in large numbers of false positives and false negatives in current approaches. Computational methods to reduce false positives are to look for over-representation of transcription factor binding sites in a set of similarly regulated promoters or to look for conservation in orthologous promoter alignments. RESULTS We have developed a novel tool, "CORE_TF" (Conserved and Over-REpresented Transcription Factor binding sites) that identifies common transcription factor binding sites in promoters of co-regulated genes. To improve upon existing binding site predictions, the tool searches for position weight matrices from the TRANSFAC R database that are over-represented in an experimental set compared to a random set of promoters and identifies cross-species conservation of the predicted transcription factor binding sites. The algorithm has been evaluated with expression and chromatin-immunoprecipitation on microarray data. We also implement and demonstrate the importance of matching the random set of promoters to the experimental promoters by GC content, which is a unique feature of our tool. CONCLUSION The program CORE_TF is accessible in a user friendly web interface at http://www.LGTC.nl/CORE_TF. It provides a table of over-represented transcription factor binding sites in the users input genes' promoters and a graphical view of evolutionary conserved transcription factor binding sites. In our test data sets it successfully predicts target transcription factors and their binding sites.
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Affiliation(s)
- Matthew S Hestand
- The Center for Human and Clinical Genetics, Leiden University Medical Center, Postzone S4-0P, PO Box 9600, 2300 RC Leiden, The Netherlands.
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4
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Heterogeneous nuclear ribonucleoprotein A/B and G inhibits the transcription of gonadotropin-releasing-hormone 1. Mol Cell Neurosci 2007; 37:69-84. [PMID: 17920292 DOI: 10.1016/j.mcn.2007.08.015] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2006] [Revised: 08/14/2007] [Accepted: 08/21/2007] [Indexed: 12/16/2022] Open
Abstract
Gonadotropin-releasing hormone 1 (GnRH1) causes the release of gonadotropins from the pituitary to control reproduction. Here we report that two heterogeneous nuclear ribonucleoproteins (hnRNP-A/B and hnRNP-G) bind to the GnRH-I upstream promoter region in a cichlid fish Astatotilapia burtoni. We identified these binding proteins using a newly developed homology based method of mass spectrometric peptide mapping. We show that both hnRNP-A/B and hnRNP-G co-localize with GnRH1 in the pre-optic area of the hypothalamus in the brain. We also demonstrated that these ribonucleoproteins exhibit similar binding capacity in vivo, using immortalized mouse GT1-7 cells where overexpression of either hnRNP-A/B or hnRNP-G significantly down-regulates GnRH1 mRNA levels in GT1-7 cells, suggesting that both act as repressors in GnRH1 transcriptional regulation.
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5
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Brooks SC, Skafar DF. From ligand structure to biological activity: modified estratrienes and their estrogenic and antiestrogenic effects in MCF-7 cells. Steroids 2004; 69:401-18. [PMID: 15219790 DOI: 10.1016/j.steroids.2004.03.014] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/24/2003] [Revised: 02/19/2004] [Accepted: 03/22/2004] [Indexed: 02/07/2023]
Abstract
A variety of compounds, including the selective estrogen receptor (ER) modulators tamoxifen and raloxifene, phytoestrogens such as genistein, and xenoestrogens such as bisphenol, bind to the estrogen receptor and elicit biological responses. Structural studies have linked the altered activity of compounds such as 4-hydroxytamoxifen, raloxifene, genistein, and tetrahydrochrysene, which have substantially different structures from estradiol (E2), to differences in the positioning of the critical "helix 12" within the ligand-binding domain (LBD) of the ER-ligand complex. However, subtle permutations of the E2 molecule would also be expected to modulate the pattern of responses within a cell. Forty-two ligands were constructed by the addition or relocation of double bonds, hydroxyl, keto, amino, and nitro substituents throughout the estra-l,3,5(10)-triene (estratriene) ring system. In this review, we summarize the effects of subtle changes in the estratriene molecule on the ability of the receptor complex to stimulate the growth of MCF-7 cells, or affect the expression of four estrogen-regulated genes (progesterone receptor, pS2 protein, cathepsin D, and tissue plasminogen activator), as well as undergo nuclear processing and downregulate ERalpha mRNA. The affinity of these ligands for, and mechanism of their binding with, the ERalpha have been measured, along with their effect on the conformation of the ER-ERE complex. In particular, two A-ring isomers of E2, 2- and 4-hydroxyestratriene-17beta-ol, display gene selective activity within MCF-7 cells which is dependent on complex endogenous promoters, an intact AF-2 and is sensitive to the level of SRC-1. Both of these A-ring isomers function as antiestrogens. Molecular modeling of these two A-ring isomers complexed with the ER ligand-binding domain supports the idea that the conformation of the LBD is affected by subtle changes in the estratriene structure.
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Affiliation(s)
- Sam C Brooks
- Department of Biochemistry and Molecular Biology, Wayne State University School of Medicine, Detroit, MI 48201, USA.
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6
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Abstract
A novel system (DBDX) was developed which allows the external surface display on filamentous bacteriophage of proteins fused to either the N- or the C-terminus of a DNA-binding protein. In conjunction with helper phage infection, expression of proteins fused to the estrogen receptor DNA-binding domain (DBD) in a phagemid vector containing the DNA sequence recognized by the DBD resulted in the production of phage particles which display the fusion protein through the phage pVIII coat on the external surface of the particle. The viability of the technique was established with several model systems: particles displaying the C-terminal domain of N-cadherin or the biotinylation domain of propionyl coenzyme A carboxylase fused to the C-terminus of the DBD were found to be bound specifically by antibody or streptavidin, respectively. Human kappa constant region cDNA was selected from a N-terminal DBD fusion lymphocyte cDNA library after two rounds of selection with anti-kappa antibody. This display system may complement currently available bacterial selection techniques.
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Affiliation(s)
- D P McGregor
- Skeletal Metabolism Research Unit, Rowett Research Institute, Greenburn Road, Bucksburn, Aberdeen, AB21 9SB, Scotland
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7
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Honda K, Shimohama S, Sawada H, Kihara T, Nakamizo T, Shibasaki H, Akaike A. Nongenomic antiapoptotic signal transduction by estrogen in cultured cortical neurons. J Neurosci Res 2001; 64:466-75. [PMID: 11391701 DOI: 10.1002/jnr.1098] [Citation(s) in RCA: 110] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Estrogen replacement therapy in menopausal women has been suggested to be beneficial in preventing the progression of cognitive impairment in Alzheimer disease. We demonstrated previously that the phosphatidylinositol 3-kinase (PI3-K)/Akt signal transduction pathway plays a pivotal role on the neuroprotection provided by 17beta-estradiol against acute glutamate toxicity. In the present study, we investigated the mechanism of neuroprotection against apoptosis because acute glutamate toxicity predominantly induced necrosis. 17beta-estradiol provided neuroprotection against apoptosis induced by staurosporine. This neuroprotection was inhibited by pretreatment with a PI3-K inhibitor, LY294002. An estrogen receptor specific antagonist, ICI182780, also suppressed the neuroprotection provided by 17beta-estradiol. Western blotting analysis demonstrated that treatment with 17beta-estradiol induced the phosphorylation of Akt within 5 min, which was suppressed by pretreatment with LY294002 and ICI182780. Furthermore, 17beta-estradiol induced phosphorylation of the cAMP response element binding protein (CREB) at Ser(133) within 15 min and then upregulated Bcl-2 in a PI3-K/Akt-dependent manner. Because CREB is known to be a transcription factor for Bcl-2, these results suggest that 17beta-estradiol exerts its antiapoptotic effects by CREB phosphorylation and Bcl-2 upregulation via nongenomic activation of the PI3-K/Akt pathway in cultured cortical neurons.
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Affiliation(s)
- K Honda
- Department of Neurology, Kyoto University Graduate School of Medicine, 54 Shogoin-Kawaharacho, Sakyo-ku, Kyoto 606-8507, Japan
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Sadakata T, Kuo C, Ichikawa H, Nishikawa E, Niu SY, Kumamaru E, Miki N. Puralpha, a single-stranded DNA binding protein, suppresses the enhancer activity of cAMP response element (CRE). BRAIN RESEARCH. MOLECULAR BRAIN RESEARCH 2000; 77:47-54. [PMID: 10814831 DOI: 10.1016/s0169-328x(00)00039-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Puralpha, a single-stranded DNA binding protein, recognizes a PUR element (GGN repeat). We have reported that Puralpha binds to a single-stranded oligonucleotide probe containing the cAMP response element (CRE) of rat somatostatin gene using a gel mobility shift assay. Here, we showed that Puralpha binds to the probe only in the presence of a PUR element by a more detailed characterization. We also examined the effects of Puralpha on the enhancer activity of the somatostatin CRE in PC12 cells using the reporter gene assay. Transfected Puralpha suppressed the CRE enhancer activity stimulated by forskolin (which increases intracellular cAMP), but suppression was not observed when the PUR element was deleted. The neurite extension induced by forskolin was inhibited by the transfection of Puralpha, but that by NGF was not suppressed. The c-fos mRNA induced by forskolin, but not by NGF, was also suppressed by Puralpha transfection. These results indicate that Puralpha suppresses the biological activities induced by forskolin, but not by NGF, in PC12 cells and that Puralpha could interfere with a cAMP-CRE signal pathway.
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Affiliation(s)
- T Sadakata
- Department of Pharmacology A6, Osaka University Medical School, 2-2 Yamadaoka, Suita, Japan
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9
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Ritchie S, Boyd FM, Wong J, Bonham K. Transcription of the human c-Src promoter is dependent on Sp1, a novel pyrimidine binding factor SPy, and can be inhibited by triplex-forming oligonucleotides. J Biol Chem 2000; 275:847-54. [PMID: 10625617 DOI: 10.1074/jbc.275.2.847] [Citation(s) in RCA: 57] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
The tyrosine kinase pp60(c-src) has been implicated in the regulation of numerous normal physiological processes as well the development of several human cancers. However, the mechanisms regulating its expression have not been addressed. In the present study, we report the presence of two Sp1/Sp3 binding sites and three polypurine:polypyrimidine (Pu:Py) tracts in the c-Src promoter that are essential for controlling expression. We demonstrate that Sp1, but not Sp3, is capable of activating the c-Src promoter and that Sp3 is also capable of inhibiting Sp1-mediated transactivation. The presence of multiple Pu:Py tracts conferred S1 sensitivity on plasmids in vitro, suggesting they are capable of adopting non B-DNA conformations. These tracts specifically bind a nuclear factor we named SPy (Src pyrimidine binding factor), which demonstrates both novel double- and single-stranded binding specificities. Mutations eliminating SPy binding compromised Src transcriptional activity, especially in concert with additional mutations affecting Sp1 binding, suggesting the two factors may cooperate in regulating c-Src expression. Finally, we demonstrate that triplex-forming oligonucleotides designed to target both Sp1 and SPy binding sites can down-regulate c-Src expression in vitro, suggesting a potential therapeutic approach to controlling c-Src expression in diseases where aberrant expression or activity has been documented.
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Affiliation(s)
- S Ritchie
- Saskatoon Cancer Center Research Unit, Saskatchewan Cancer Agency. Division of Oncology, University of Saskatchewan, Saskatoon, Saskatchewan S7N 4H4, Canada
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10
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Driscoll MD, Sathya G, Saidi LF, DeMott MS, Hilf R, Bambara RA. An explanation for observed estrogen receptor binding to single-stranded estrogen-responsive element DNA. Mol Endocrinol 1999; 13:958-68. [PMID: 10379894 DOI: 10.1210/mend.13.6.0296] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Estrogen-inducible genes contain an enhancer called the estrogen response element (ERE), a double-stranded inverted repeat. The estrogen receptor (ER) is generally thought to bind to the double-stranded ERE. However, some reports provide evidence that an ER homodimer can bind a single strand of the ERE and suggest that single-stranded ERE binding is the preferred binding mode for ER. Since these two models describe quite different mechanisms of receptor action, we have attempted to reconcile the observations. Analyzing DNA structure by nuclease sensitivity, we found that two identical molecules of a single strand of DNA containing the ERE sequence can partially anneal in an antiparallel manner. Bimolecular annealing produces double-stranded inverted repeats, with adjacent unannealed tails. The amount of annealing correlates exactly with the ability of ER to bind bimolecular EREs. Either strand of an ERE could anneal to itself in a way that would bind ER. We conclude that ER binds only the annealed double-stranded ERE both in vitro and in vivo.
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Affiliation(s)
- M D Driscoll
- Department of Biochemistry and Biophysics, The University of Rochester School of Medicine and Dentistry, New York 14642, USA
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11
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Chau KY, Lam HY, Lee KL. Estrogen treatment induces elevated expression of HMG1 in MCF-7 cells. Exp Cell Res 1998; 241:269-72. [PMID: 9633537 DOI: 10.1006/excr.1998.4052] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The high mobility group (HMG) 1 protein is a highly conserved and ubiquitous chromosomal protein found enriched in active chromatin. In this study, we have investigated the effect of estrogen on the expression of the human high mobility group protein HMG1 gene and found that the HMG1 mRNA level in MCF-7 cells was sharply increased 2.5-fold after 30 min of estrogen treatment. Under continuous estrogen treatment, the HMG1 mRNA level decreased to a 1.5 times that of the basal level at 90 min and remained at this elevated level under estrogen treatment for up to 24 h. These results support the recent finding by Verrier et al. (C.S. Verrier, 1997, Mol. Endocrinol. 11, 1009-1019) that HMG1 promotes the binding of the estrogen receptor to the estrogen response element and further reinforce our believe that HMG1 plays a significant role in estrogen-induced gene expression.
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Affiliation(s)
- K Y Chau
- Department of Applied Biology and Chemical Technology, Hong Kong Polytechnic University, Kowloon, Hong Kong
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12
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Budhram-Mahadeo V, Parker M, Latchman DS. POU transcription factors Brn-3a and Brn-3b interact with the estrogen receptor and differentially regulate transcriptional activity via an estrogen response element. Mol Cell Biol 1998; 18:1029-41. [PMID: 9448000 PMCID: PMC108815 DOI: 10.1128/mcb.18.2.1029] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/1997] [Accepted: 11/19/1997] [Indexed: 02/05/2023] Open
Abstract
The estrogen receptor (ER) modulates transcription by forming complexes with other proteins and then binding to the estrogen response element (ERE). We have identified a novel interaction of this receptor with the POU transcription factors Brn-3a and Brn-3b which was independent of ligand binding. By pull-down assays and the yeast two-hybrid system, the POU domain of Brn-3a and Brn-3b was shown to interact with the DNA-binding domain of the ER. Brn-3-ER interactions also affect transcriptional activity of an ERE-containing promoter, such that in estradiol-stimulated cells, Brn-3b strongly activated the promoter via the ERE, while Brn-3a had a mild inhibitory effect. The POU domain of Brn-3b which interacts with the ER was sufficient to confer this activation potential, and the change of a single amino acid in the first helix of the POU homeodomain of Brn-3a to its equivalent in Brn-3b can change the mild repressive effect of Brn-3a to a stimulatory Brn-3b-like effect. These observations and their implications for transcriptional regulation by the ER are discussed.
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Affiliation(s)
- V Budhram-Mahadeo
- Department of Molecular Pathology, The Windeyer Institute of Medical Sciences, University College Medical School, London, United Kingdom
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13
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Thomas T, Kulkarni GD, Gallo MA, Greenfield N, Lewis JS, Shirahata A, Thomas TJ. Effects of natural and synthetic polyamines on the conformation of an oligodeoxyribonucleotide with the estrogen response element. Nucleic Acids Res 1997; 25:2396-402. [PMID: 9171091 PMCID: PMC146762 DOI: 10.1093/nar/25.12.2396] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
We studied the effects of natural and synthetic polyamines on the conformation of an oligodeoxyribonucleotide (ODN1) harboring the estrogen response element (ERE) by circular dichroism (CD) spectroscopy and polyacrylamide gel electrophoresis. Putrescine and spermidine had no marked effect on the CD spectrum of ODN1. In contrast, spermine provoked and stabilized two characteristic changes in the CD spectrum. The first change was indicated by an increase in the intensity of the CD band at 280 nm at 0.5 mM spermine in Tris-HCl buffer containing 50 mM NaCl. This change appears to be related to changes in base tilt and conformational alterations similar to A-DNA. At 1-2 mM spermine, the CD spectrum was characterized by a loss of positive bands at 220 and 270 nm. This change might have contributions from polyamine-induced condensation/aggregation of DNA. Spectral measurements were also conducted in Tris-HCl buffer containing 150 mM NaCl to minimize contributions from condensation and aggregation of ODN1. Under these conditions, CD spectral changes were retained by (ODN1), although the magnitude of the change was diminished. In contrast, a control oligdeoxyribonucleotide (ODN2) having similar base composition did not show any significant change in the CD spectrum in the presence of 150 mM NaCl and 2 mM spermine. The changes in the CD spectrum of ODN1 were highly sensitive to polyamine structure, as evidenced by experiments using spermine analogs with altered number of -CH2- groups separating the amino and imino groups. Electrophoretic mobility shift analysis further showed ODN1 stabilization by spermine and its analogs. These data demonstrate the ability of an ODN containing ERE to undergo conformational transitions in the presence of polyamines and suggest a possible mechanism for polyamine-mediated alterations in the interaction of estrogen receptor with ERE.
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Affiliation(s)
- T Thomas
- Department of Environmental and Community Medicine, University of Medicine and Dentistry of New Jersey-Robert Wood Johnson Medical School, New Brunswick, NJ 08903, USA
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14
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Liu B, Maul RS, Kaetzel DM. Repression of platelet-derived growth factor A-chain gene transcription by an upstream silencer element. Participation by sequence-specific single-stranded DNA-binding proteins. J Biol Chem 1996; 271:26281-90. [PMID: 8824279 DOI: 10.1074/jbc.271.42.26281] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Platelet-derived growth factor A-chain is a potent mitogen expressed in a restricted number of normal and transformed cells. Transient transfection and deletion analysis in BSC-1 (African green monkey, renal epithelial) cells revealed that the -1680 to -1374 region of the A-chain gene repressed homologous and heterologous promoter activities by 60-80%. An S1 nuclease-hypersensitive region (5'SHS) was identified within this region (-1418 to -1388) that exhibited transcriptional silencer activity in BSC-1 and a variety of human tumor cell lines (U87, HepG2, and HeLa). Electrophoretic mobility shift assays conducted with 5'SHS oligodeoxynucleotide probes revealed several binding protein complexes that displayed unique preferences for binding to sense, antisense, and double-stranded forms of the element. Southwestern blot analysis revealed that the antisense strand of 5'SHS binds to nuclear proteins of molecular mass 97, 87, 44, and 17 kDa, whereas the double-stranded form of 5'SHS is recognized by a 70-kDa factor. Mutations within 5'SHS element indicated the necessity of a central 5'-GGGGAGGGGG-3' motif for protein binding and silencer function, while nucleotides flanking both sides of the motif were also critical for repression. These results support a model in which silencer function of 5'SHS is mediated by antisense strand binding proteins, possibly by stabilizing single-stranded DNA conformations required for interaction with enhancer sequences in the proximal promoter region of the A-chain gene.
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Affiliation(s)
- B Liu
- Department of Pharmacology, University of Kentucky Medical Center, Lexington, Kentucky 40536, USA
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Xu G, Goodridge AG. Characterization of a polypyrimidine/polypurine tract in the promoter of the gene for chicken malic enzyme. J Biol Chem 1996; 271:16008-19. [PMID: 8663263 DOI: 10.1074/jbc.271.27.16008] [Citation(s) in RCA: 25] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Starvation inhibits and refeeding stimulates transcription of the malic enzyme gene in chick liver. DNA between -320 and +72 base pairs (bp) is DNase I-hypersensitive in hepatic nuclei from fed but not starved chicks (Ma, X. J., and Goodridge, A. G. (1992) Nucleic Acids Res. 20, 4997-5002). A polypyrimidine/polypurine (PPY/PPU) tract lies within the DNase I-hypersensitive region. In hepatocytes transiently transfected with plasmids containing triiodothyronine response elements and a minimal promoter from the malic enzyme gene linked to the chloramphenicol acetyltransferase gene, deletion of the PPY/PPU tract inhibited chloramphenicol acetyltransferase activity by about 90% with or without triiodothyronine. Fine mapping of S1 nuclease-sensitive sites suggests that the PPY/PPU tract can assume different isoforms of non-B-DNA, some of which may be triplex structures. The PPY/PPU tract contains specific binding sites for single- and double-stranded DNA binding proteins and, with 8 bp 3' of the tract, can function as a promoter. A (CT)7 repeat binds single-stranded DNA-binding protein and is essential for promoter activity. Two C-rich elements bind single-stranded DNA-binding proteins and may mediate inhibition of promoter function. The single- and double-stranded DNA-binding proteins that interact with the PPY/PPU tract may regulate transcription of the malic enzyme gene.
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Affiliation(s)
- G Xu
- Department of Biochemistry, University of Iowa, Iowa City, Iowa 52240, USA
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Giffin W, Haché RJ. Nuclear factor binding to a DNA sequence element that represses MMTV transcription induces a structural transition and leads to the contact of single-stranded binding proteins with DNA. DNA Cell Biol 1995; 14:1025-35. [PMID: 8534369 DOI: 10.1089/dna.1995.14.1025] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
NRE1 is a DNA sequence element in the long terminal repeat of mouse mammary tumor virus through which viral transcription is repressed. In addition to double-stranded DNA binding, both upper- and lower-stranded NRE1 binding activities occur in nuclear extracts. All three binding activities appear to be important for transcriptional effects. We report that occupancy of NRE1 within linear double-stranded NRE1 induces a structural transition in upstream flanking DNA that is facilitated by Mg2+. This transition was reflected by the striking DNase I sensitivity of the DNA. As Mg2+ concentration was increased, discrete DNase I hypersensitivity on one face of the DNA progressed to complete degradation of template. On the DNA face opposite the DNase I hypersensitivity, Mg2+ promoted regularly spaced cleavage by the single-strand-specific cleavage agents KMnO4 and S1 nuclease. Induction of degradation by DNase I occurred independently of MMTV sequences flanking NRE1, because nuclear extract-dependent DNase I sensitivity was conferred to an unrelated DNA fragment by introduction of a 23-bp NRE1-containing oligonucleotide. UV protein-DNA cross-linking revealed that addition of Mg2+ to a double-stranded NRE1 DNA binding assay induced conversion from a double- to a single-stranded protein-DNA cross-linking pattern. Thus, nuclear factor binding to NRE1 induces changes in DNA topology that promote the direct contact of single-stranded NRE1 binding factors with DNA.
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Affiliation(s)
- W Giffin
- Department of Medicine, University of Ottawa, Loeb Institute for Medical Research, Ottawa Civic Hospital, Ontario, Canada
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17
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Haas S, Thatikunta P, Steplewski A, Johnson EM, Khalili K, Amini S. A 39-kD DNA-binding protein from mouse brain stimulates transcription of myelin basic protein gene in oligodendrocytic cells. J Biophys Biochem Cytol 1995; 130:1171-9. [PMID: 7657701 PMCID: PMC2120554 DOI: 10.1083/jcb.130.5.1171] [Citation(s) in RCA: 75] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
The MB1 regulatory sequence of the myelin basic protein (MBP) gene spanning between nucleotides -14 to -50 with respect to the transcription start site is critical for cell type-specific transcription of the MBP gene, which encodes the major protein component of myelin sheath in cells derived from the central nervous system (CNS). This regulatory sequence has the ability to interact with a developmentally controlled DNA-binding protein from mouse brain that stimulates transcription of MBP promoter in an in vitro system (Haas, S., J. Gordon, and K. Khalili. 1993. Mol. Cell. Biol. 13:3103-3112). Here, we report the purification of a 39-kD protein from mouse brain tissue at the peak of myelination and MBP production that binds to the MB1 regulatory motif. Following partial amino acid sequence analysis, we have identified a complementary DNA encoding a 39-kD DNA-binding protein called pur alpha. Expression of pur alpha cDNA in the prokaryotic and eukaryotic cells resulted in the synthesis of a protein with characteristics similar to the purified brain-derived 39-kD protein in band shift competition assays. Cotransfection of the recombinant pur alpha expressor plasmid with MBP promoter construct indicated that Pur alpha stimulates transcription of the MBP promoter in oligodendrocytic cells, and that the nucleotide sequence required for binding of the 39-kD Pur alpha to DNA within the MB1 region is crucial for this activity. Moreover, transient expression of Pur alpha caused elevation in the level of endogenous MBP RNA in oligodendrocytic cells. Thus, Pur alpha, a sequence-specific DNA-binding protein upon binding to MB1 regulatory region may play a significant role in determining the cell type-specific expression of MBP in brain.
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Affiliation(s)
- S Haas
- Jefferson Institute of Molecular Medicine, Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, Pennsylvania 19107, USA
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18
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Smidt MP, Russchen B, Snippe L, Wijnholds J, Ab G. Cloning and characterisation of a nuclear, site specific ssDNA binding protein. Nucleic Acids Res 1995; 23:2389-95. [PMID: 7630716 PMCID: PMC307042 DOI: 10.1093/nar/23.13.2389] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Estradiol inducible, liver-specific expression of the apoVLDL II gene is mediated through the estrogen receptor and a variety of other DNA-binding proteins. In the present study we report the cloning and characterisation of a single-strand DNA binding protein that interacts with the lower strand of a complex regulatory site, which includes the major estrogen responsive element and a site that resembles the rat albumin site D (apoVLDL II site D). Based on its binding specificity determined with electro-mobility shift assays, the protein is named single-strand D-box binding factor (ssDBF). Analysis of the deduced 302 amino acid sequence revealed that the protein belongs to the heteronuclear ribonucleoprotein A/B family (hnRNP A/B) and resembles other known eukaryotic single-strand DNA binding proteins. Transient transfection experiments in a chicken liver cell-line showed that the protein represses estrogen-induced transcription. A protein with similar binding characteristics is present in liver nuclear extract. The relevance of the occurrence of this protein to the expression of the apoVLDL II gene is discussed.
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Affiliation(s)
- M P Smidt
- Laboratory of Biochemistry, University of Groningen, The Netherlands
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19
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Haas S, Steplewski A, Siracusa LD, Amini S, Khalili K. Identification of a sequence-specific single-stranded DNA binding protein that suppresses transcription of the mouse myelin basic protein gene. J Biol Chem 1995; 270:12503-10. [PMID: 7539003 DOI: 10.1074/jbc.270.21.12503] [Citation(s) in RCA: 47] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
The myelin basic protein (MBP) gene is expressed only in oligodendrocytes and Schwann cells, and expression follows a tightly regulated developmental time course. Cell type- and developmental stage-specific expression of the MBP gene appears to be regulated by a series of cis-acting elements located upstream of the transcription start site. The proximal element of the MBP regulatory region (MB1), located between nucleotides -14 and -50, is one of several elements participating in the programmed expression of MBP. In this report, we describe the molecular cloning and characterization of myelin gene expression factor-2 (Myef-2), a protein isolated from mouse brain that binds specifically to single-stranded DNA derived from the MB1 element and represses transcription of the MBP gene in transient transfection assay. Myef-2 mRNA is developmentally regulated in mouse brain; its peak expression occurs at postnatal day 7, prior to the onset of MBP expression. The developmental pattern of Myef-2 mRNA expression coincides with that previously described for SCIP, a POU domain transcription factor that also represses myelin basic protein expression. The myef-2 gene maps to mouse chromosome 2. The relevance of these findings for regulation of MBP gene expression and oligodendrocyte differentiation is discussed.
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Affiliation(s)
- S Haas
- Jefferson Institute of Molecular Medicine, Department of Biochemistry and Molecular Biology, Thomas-Jefferson University, Philadelphia, Pennsylvania 19107, USA
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20
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Friend KE, Ang LW, Shupnik MA. Estrogen regulates the expression of several different estrogen receptor mRNA isoforms in rat pituitary. Proc Natl Acad Sci U S A 1995; 92:4367-71. [PMID: 7753813 PMCID: PMC41945 DOI: 10.1073/pnas.92.10.4367] [Citation(s) in RCA: 103] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
A 5.2-kb mRNA band that contains estrogen receptor (ER) sequence and exhibits sex- and tissue-specific expression has been identified in rat pituitary via Northern analysis; this band is composed of at least two distinctive ER mRNA isoforms. This mRNA is expressed in high levels in female pituitary but is absent in male pituitary and uterus, whereas the mRNA encoding the full-length receptor (6.2 kb) is expressed in all the aforementioned tissues. Estradiol treatment potently induces the expression of the 5.2-kb band in the male pituitary. Oligonucleotide hybridization and ribonuclease-protection experiments indicate that the pituitary ER variant is missing exons 1-4. Two corresponding cDNA clones, truncated estrogen receptor product 1 and 2 (TERP-1 and TERP-2), were isolated by using the anchored PCR. Both sequences contain a 31-bp segment of specific sequence upstream of exon 5; TERP-2, however, contains an additional 66 bp of specific sequence between the 31-bp segment and exon 5. On Northern analysis, probes complementary to the 31-bp segment of specific sequence hybridize only to the 5.2-kb band. Immunoblotting identified several proteins in rat pituitary that could represent the translation products of these or related transcripts. In summary, several ER isoforms have been identified that exhibit both tissue-specific expression and marked estrogen regulation and differ from full-length receptor by virtue of sequence upstream of the exon 4/5 boundary. Physiologically, the putative proteins encoded by these or similar isoforms might be important modulators of the tissue- and promoter-specific effects of estradiol.
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Affiliation(s)
- K E Friend
- Department of Medicine, University of Virginia Medical Center, Charlottesville 22903, USA
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21
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Mukherjee B, Burma S, Hasnain SE. The 30-kDa protein binding to the "initiator" of the baculovirus polyhedrin promoter also binds specifically to the coding strand. J Biol Chem 1995; 270:4405-11. [PMID: 7876205 DOI: 10.1074/jbc.270.9.4405] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
We previously reported the purification and characterization of the polyhedrin promoter-binding protein (PPBP), an unusual DNA-binding protein that interacts with transcriptionally important motifs of the baculovirus polyhedrin gene promoter (S. Burma, B. Mukherjee, A. Jain, S. Habib, and S.E. Hasnain, J. Biol. Chem. (1994) 269, 2750-2757. PPBP also exhibits a sequence-specific single-stranded DNA-binding activity. Gel retardations and competition analyses with double- and single-stranded oligonucleotides indicated that PPBP binds the coding strand and not the noncoding strand of the promoter. This was further confirmed by UV cross-linking and Southwestern blotting experiments. Gel retardations with mutated oligonucleotides indicated that both dsDNA and ssDNA binding involve common AATA-AATAAGTATT motifs. However, ssDNA binding is dependent upon ionic interactions unlike dsDNA binding, which is mainly through nonionic interactions. The affinity of PPBP for the coding strand appears to be higher than that for duplex promoter DNA. Interestingly, the PPBP-coding strand complex has a longer half-life (approximately 60 min) than the PPBP-duplex promoter complex (approximately 15 min). PPBP represents a unique example of an "initiator" promoter-binding protein with dual dsDNA and ssDNA binding activities, and this reconciles very well with the unusual binding characteristics displayed by it. The formation of the PPBP-coding strand complex in vivo may be a crucial step for the exceptionally high and repeated rounds of transcriptional activity of the baculovirus polyhedrin gene promoter.
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Affiliation(s)
- B Mukherjee
- Eukaryotic Gene Expression Laboratory, National Institute of Immunology, New Delhi, India
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22
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Tanuma Y, Nakabayashi H, Esumi M, Endo H. A silencer element for the lipoprotein lipase gene promoter and cognate double- and single-stranded DNA-binding proteins. Mol Cell Biol 1995; 15:517-23. [PMID: 7799960 PMCID: PMC232003 DOI: 10.1128/mcb.15.1.517] [Citation(s) in RCA: 27] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
Transfection experiments with constructs containing various 5'-deleted fragments of the human lipoprotein lipase (LPL) promoter and the chloramphenicol acetyltransferase reporter gene revealed an LPL silencer element (LSE) in the region of nucleotides -225 to -81 of the LPL gene that functioned in Chinese hamster ovary (CHO) and HeLa cells. Gel retardation competition analysis showed the presence of a nuclear factor(s) capable of binding to the sequence of nucleotides -169 to -152 of LSE (LSE-6) in a single-stranded (opposite-strand) and double-stranded specific fashion, the binding affinity being almost the same in the two binding forms. Site-directed mutagenesis indicated that almost the entire sequence of LSE-6 was necessary to form the complexes and also critical for silencing activity in CHO cells. The amounts of this binding factor(s) in CHO and HeLa cells were closely associated with transcriptional silencing activity. Photochemical cross-linking experiments indicated that the single- and double-stranded elements recognized the same binding factor(s) with molecular masses of 54 to 63 kDa and 109 to 124 kDa. The 109- to 124-kDa DNA binding factor(s) was found to be a doublet of that of the 54- to 63-kDa factor by isoelectric focusing or by increasing the time of exposure to UV irradiation. When inserted upstream of another gene such as that of the simian virus 40 enhancer/promoter of pSV2CAT, the sequence of nucleotides -190 to -143 (LSE-1) also suppressed transcription of the reporter gene in CHO cells. These results strongly suggest that the LSE plays a role in regulation of LPL gene expression by suppressing its transcription.
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Affiliation(s)
- Y Tanuma
- Medical Research Institute, Nihon University School of Medicine, Tokyo, Japan
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23
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Eid JE, Sollner-Webb B. ST-1, a 39-kilodalton protein in Trypanosoma brucei, exhibits a dual affinity for the duplex form of the 29-base-pair subtelomeric repeat and its C-rich strand. Mol Cell Biol 1995; 15:389-97. [PMID: 7799947 PMCID: PMC231977 DOI: 10.1128/mcb.15.1.389] [Citation(s) in RCA: 27] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
In our attempt to identify telomere region-binding proteins in Trypanosoma brucei, we identified ST-1, a polypeptide with novel features. ST-1 was chromatographically purified from S-100 cell extracts and was renatured from a sodium dodecyl sulfate-protein gel as a 39-kDa polypeptide. It forms a specific complex with the trypanosome telomere repeats of TTAGGG, but more significantly, it shows a higher affinity for the 29-bp subtelomere repeats of T. brucei. These 29-mer boxes are a large tandem series of telomere-derived repeats which separate the simple telomere DNA from middle-repetitive telomere-associated sequences on many chromosomes. ST-1 is the first example of a protein binding within such large repetitive subtelomere elements in trypanosomes or other organisms. ST-1 is also novel in that it has a selective affinity for the C-rich strands of both the subtelomeric 29-mer and the telomere repeats, comparable to that for the duplex form of the respective repeats. All previously described telomere-binding proteins have affinity for only the duplex form or for the G-rich strand. This C-rich strand binding specificity of ST-1 may provide insight into this protein's mechanism of binding in vivo.
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Affiliation(s)
- J E Eid
- Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205
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24
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The DNA-bending protein HMG-1 enhances progesterone receptor binding to its target DNA sequences. Mol Cell Biol 1994. [PMID: 8164686 DOI: 10.1128/mcb.14.5.3376] [Citation(s) in RCA: 140] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Steroid hormone receptors are ligand-dependent transcriptional activators that exert their effects by binding as dimers to cis-acting DNA sequences termed hormone response elements. When human progesterone receptor (PR), expressed as a full-length protein in a baculovirus system, was purified to homogeneity, it retained its ability to bind hormonal ligand and to dimerize but exhibited a dramatic loss in DNA binding activity for specific progesterone response elements (PREs). Addition of nuclear extracts from several cellular sources restored DNA binding activity, suggesting that PR requires a ubiquitous accessory protein for efficient interaction with specific DNA sequences. Here we have demonstrated that the high-mobility-group chromatin protein HMG-1, as a highly purified protein, dramatically enhanced binding of purified PR to PREs in gel mobility shift assays. This effect appeared to be highly selective for HMG-1, since a number of other nonspecific proteins failed to enhance PRE binding. Moreover, HMG-1 was effective when added in stoichiometric amounts with receptor, and it was capable of enhancing the DNA binding of both the A and B amino-terminal variants of PR. The presence of HMG-1 measurably increased the binding affinity of purified PR by 10-fold when a synthetic palindromic PRE was the target DNA. The increase in binding affinity for a partial palindromic PRE present in natural target genes was greater than 10-fold. Coimmunoprecipitation assays using anti-PR or anti-HMG-1 antibodies demonstrated that both PR and HMG-1 are present in the enhanced complex with PRE. HMG-1 protein has two conserved DNA binding domains (A and B), which recognize DNA structure rather than specific sequences. The A- or B-box domain expressed and purified from Escherichia coli independently stimulated the binding of PR to PRE, and the B box was able to functionally substitute for HMG-1 in enhancing PR binding. DNA ligase-mediated ring closure assays demonstrated that both the A and B binding domains mediate DNA flexure. It was also demonstrated in competition binding studies that the intact HMG-1 protein binds to tightly curved covalently closed or relaxed DNA sequences in preference to the same sequence in linear form. The finding that enhanced PRE binding was intrinsic to the HMG-1 box, combined with the demonstration that HMG-1 or its DNA binding boxes can flex DNA, suggests that HMG-1 facilitates the binding of PR by inducing a structural change in the target DNA.
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25
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Oñate SA, Prendergast P, Wagner JP, Nissen M, Reeves R, Pettijohn DE, Edwards DP. The DNA-bending protein HMG-1 enhances progesterone receptor binding to its target DNA sequences. Mol Cell Biol 1994; 14:3376-91. [PMID: 8164686 PMCID: PMC358703 DOI: 10.1128/mcb.14.5.3376-3391.1994] [Citation(s) in RCA: 47] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
Steroid hormone receptors are ligand-dependent transcriptional activators that exert their effects by binding as dimers to cis-acting DNA sequences termed hormone response elements. When human progesterone receptor (PR), expressed as a full-length protein in a baculovirus system, was purified to homogeneity, it retained its ability to bind hormonal ligand and to dimerize but exhibited a dramatic loss in DNA binding activity for specific progesterone response elements (PREs). Addition of nuclear extracts from several cellular sources restored DNA binding activity, suggesting that PR requires a ubiquitous accessory protein for efficient interaction with specific DNA sequences. Here we have demonstrated that the high-mobility-group chromatin protein HMG-1, as a highly purified protein, dramatically enhanced binding of purified PR to PREs in gel mobility shift assays. This effect appeared to be highly selective for HMG-1, since a number of other nonspecific proteins failed to enhance PRE binding. Moreover, HMG-1 was effective when added in stoichiometric amounts with receptor, and it was capable of enhancing the DNA binding of both the A and B amino-terminal variants of PR. The presence of HMG-1 measurably increased the binding affinity of purified PR by 10-fold when a synthetic palindromic PRE was the target DNA. The increase in binding affinity for a partial palindromic PRE present in natural target genes was greater than 10-fold. Coimmunoprecipitation assays using anti-PR or anti-HMG-1 antibodies demonstrated that both PR and HMG-1 are present in the enhanced complex with PRE. HMG-1 protein has two conserved DNA binding domains (A and B), which recognize DNA structure rather than specific sequences. The A- or B-box domain expressed and purified from Escherichia coli independently stimulated the binding of PR to PRE, and the B box was able to functionally substitute for HMG-1 in enhancing PR binding. DNA ligase-mediated ring closure assays demonstrated that both the A and B binding domains mediate DNA flexure. It was also demonstrated in competition binding studies that the intact HMG-1 protein binds to tightly curved covalently closed or relaxed DNA sequences in preference to the same sequence in linear form. The finding that enhanced PRE binding was intrinsic to the HMG-1 box, combined with the demonstration that HMG-1 or its DNA binding boxes can flex DNA, suggests that HMG-1 facilitates the binding of PR by inducing a structural change in the target DNA.
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Affiliation(s)
- S A Oñate
- Department of Pathology, University of Colorado Cancer Center, Denver 80262
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26
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Yamazoe M, Shirahige K, Rashid M, Kaneko Y, Nakayama T, Ogasawara N, Yoshikawa H. A protein which binds preferentially to single-stranded core sequence of autonomously replicating sequence is essential for respiratory function in mitochondrial of Saccharomyces cerevisiae. J Biol Chem 1994. [DOI: 10.1016/s0021-9258(17)36598-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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27
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Interaction of two sequence-specific single-stranded DNA-binding proteins with an essential region of the beta-casein gene promoter is regulated by lactogenic hormones. Mol Cell Biol 1994. [PMID: 8246951 DOI: 10.1128/mcb.13.12.7303] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Transcription of the beta-casein gene in mammary epithelial cells is regulated by the lactogenic hormones insulin, glucocorticoids, and prolactin. The DNA sequence elements in the promoter which confer the action of the hormones on the transcriptional machinery and the nuclear proteins binding to this region have been investigated. We found that 221 nucleotides of promoter sequence 5' of the RNA start site are sufficient to mediate the induction of a chloramphenicol acetyltransferase reporter gene in transfected HC11 mammary epithelial cells. Deletion of 5' sequences to position -183 results in a construct with enhanced basal activity which still retains inducibility. A -170 beta-casein promoter-chloramphenicol acetyltransferase construct has very low transcriptional activity, which indicates the presence of a negative regulatory in the region between -221 and -183 and a positive regulatory element between -183 and -170. Band shift analysis showed that the promoter region between -194 and -163 specifically binds two nuclear proteins. The proteins are sequence-specific, single-stranded DNA-binding proteins which exclusively recognize the upper DNA strand and most likely play a repressing role in transcription. DNA binding activity of these nuclear proteins was observed only in nuclear extracts from mammary glands of mice in late pregnancy and postlactation, not during lactation. Hormonal control of the DNA binding activity of these proteins was also observed in the mammary epithelial cell line HC11. Mixing experiments showed that extracts from mammary tissue of lactating mice and from lactogenic hormone-treated HC11 cells contain an activity which can suppress the DNA binding of the single-stranded DNA-binding proteins.2+ identical specificity to the single-stranded DNA.
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28
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Giffin W, Torrance H, Saffran H, MacLeod H, Haché R. Repression of mouse mammary tumor virus transcription by a transcription factor complex. Binding of individual components to separated DNA strands. J Biol Chem 1994. [DOI: 10.1016/s0021-9258(17)42278-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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29
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Bolander FF. Hormonally Regulated Transcription Factors. Mol Endocrinol 1994. [DOI: 10.1016/b978-0-12-111231-8.50017-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022] Open
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30
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Altiok S, Groner B. Interaction of two sequence-specific single-stranded DNA-binding proteins with an essential region of the beta-casein gene promoter is regulated by lactogenic hormones. Mol Cell Biol 1993; 13:7303-10. [PMID: 8246951 PMCID: PMC364801 DOI: 10.1128/mcb.13.12.7303-7310.1993] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
Transcription of the beta-casein gene in mammary epithelial cells is regulated by the lactogenic hormones insulin, glucocorticoids, and prolactin. The DNA sequence elements in the promoter which confer the action of the hormones on the transcriptional machinery and the nuclear proteins binding to this region have been investigated. We found that 221 nucleotides of promoter sequence 5' of the RNA start site are sufficient to mediate the induction of a chloramphenicol acetyltransferase reporter gene in transfected HC11 mammary epithelial cells. Deletion of 5' sequences to position -183 results in a construct with enhanced basal activity which still retains inducibility. A -170 beta-casein promoter-chloramphenicol acetyltransferase construct has very low transcriptional activity, which indicates the presence of a negative regulatory in the region between -221 and -183 and a positive regulatory element between -183 and -170. Band shift analysis showed that the promoter region between -194 and -163 specifically binds two nuclear proteins. The proteins are sequence-specific, single-stranded DNA-binding proteins which exclusively recognize the upper DNA strand and most likely play a repressing role in transcription. DNA binding activity of these nuclear proteins was observed only in nuclear extracts from mammary glands of mice in late pregnancy and postlactation, not during lactation. Hormonal control of the DNA binding activity of these proteins was also observed in the mammary epithelial cell line HC11. Mixing experiments showed that extracts from mammary tissue of lactating mice and from lactogenic hormone-treated HC11 cells contain an activity which can suppress the DNA binding of the single-stranded DNA-binding proteins.2+ identical specificity to the single-stranded DNA.
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Affiliation(s)
- S Altiok
- Friedrich Miescher Institute, Basel, Switzerland
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31
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Schwartz JA, Skafar DF. Ligand-mediated modulation of estrogen receptor conformation by estradiol analogs. Biochemistry 1993; 32:10109-15. [PMID: 8399136 DOI: 10.1021/bi00089a029] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
The studies presented here show how changing the structure of the ligand can affect the conformation of the receptor. Five different estradiol analogs have been tested for binding to the calf uterine estrogen receptor. In three of the analogs the phenolic hydroxyl group had been moved from the 3 to the 1, 2, or 4 position on the A-ring (1-hydroxyestratrien-17 beta-ol, 2-hydroxyestratrien-17 beta-ol, or 4-hydroxyestratrien-17 beta-ol). In the remaining two analogs either the A- or the D-ring hydroxyl group had been removed altogether (estratrien-17 beta-ol or 3-hydroxyestratriene). Competition binding assay showed that the relative binding affinity for the estrogen receptor had been weakened by all changes in the structure of the ligand. Furthermore, the ligands in which either the 3 beta- or the 17 beta-hydroxyl group was missing produced nonparallel slopes in the linear portions of the displacement curves compared to that of estradiol; the ligands in which the phenolic hydroxyl had simply been moved around the A-ring, however, did not. These observations implied that the receptor binding mechanism used by the monohydroxyl ligands was different from that of estradiol. Saturation binding analysis showed that while the presence of any of the dihydroxyl ligands or that of estratrien-17 beta-ol decreased the positive cooperativity of the [3H]estradiol-estrogen receptor interaction, the presence of the 3-hydroxyestratriene ligand increased it. These results suggest that both the binding mechanism and the affinity of the ligand for the receptor are exquisitely sensitive to the structure of the ligand.
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Affiliation(s)
- J A Schwartz
- Department of Physiology, Wayne State University School of Medicine, Detroit, Michigan 48201
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32
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Mukherjee R. Selective binding of the estrogen receptor to one strand of the estrogen responsive element. Nucleic Acids Res 1993; 21:2655-61. [PMID: 8332462 PMCID: PMC309595 DOI: 10.1093/nar/21.11.2655] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
The human estrogen receptor (hER) activates gene transcription by binding to cognate palindromic sequences called estrogen responsive elements (ERE). I used gel retardation assays and oligonucleotides containing the ERE from the Xenopus vitellogenin gene to study the interaction of the hER with the ERE. I observed that the hER bound to double-stranded ERE and to the single strand of the ERE that had T in the center with nearly equal affinity, but not to the strand which had A in the center. Interchanging the two central nucleotides changed the strand specificity. Binding of the hER to a single strand is extremely sensitive to temperature. Initial recognition of one of the two strands of the ERE may be involved in the binding of the hER to the ERE.
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Affiliation(s)
- R Mukherjee
- Laboratoire de Génétique Moléculaire des Eucaryotes du CNRS, Unité 184 de Biologie Moléculaire et de Génie Génétique de l'INSERM, Strasbourg, France
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33
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A complex array of double-stranded and single-stranded DNA-binding proteins mediates induction of the ovalbumin gene by steroid hormones. J Biol Chem 1993. [DOI: 10.1016/s0021-9258(19)38637-5] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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34
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Thomas T, Thomas TJ. Structural specificity of polyamines in modulating the binding of estrogen receptor to potential Z-DNA forming sequences. JOURNAL OF RECEPTOR RESEARCH 1993; 13:1115-33. [PMID: 8254578 DOI: 10.3109/10799899309063267] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Estrogen receptor (ER) is a gene-regulatory protein that mediates the action of estradiol. In order to examine the role of conformational dynamics of DNA in estrogenic regulation of gene expression, we studied the binding of ER to poly(dA-dC).poly(dG-dT) which undergoes transition to a left-handed Z-DNA form. This type of dinucleotide repeats are widely distributed in mammalian genome and are present in estrogen response elements. Binding affinity of ER for the polynucleotide was assessed by its ability to release ER bound to DNA-cellulose. ER binding by poly(dA-dC).poly(dG-dT) was enhanced in the presence of an endogenous polyamine, spermidine, H2N(CH2)4NH(CH2)3NH2. The concentration of spermidine required for facilitating 50% elution of ER (EC50) was 75 microM. This EC50 increased to 500 microM for a spermidine homolog, H2N(CH2)8NH(CH2)3NH2, demonstrating polyamine structural specificity. Spectroscopic measurements showed that the presence of 100-200 microM spermidine initiated changes in the conformation of the polynucleotide indicative of Z-DNA form, but a major alteration to Z-DNA spectrum occurred only at 300 microM concentration. These data suggest that ER favors DNA sequences poised for Z-DNA transition. The efficacy of spermidine homologs in facilitating ER-DNA interaction may be important in predicting their efficiency to replace cellular functions of spermidine.
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Affiliation(s)
- T Thomas
- Department of Environmental and Community Medicine, University of Medicine and Dentistry of New Jersey-Robert Wood Johnson Medical School, Piscataway 08854
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35
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Price CM, Skopp R, Krueger J, Williams D. DNA recognition and binding by the Euplotes telomere protein. Biochemistry 1992; 31:10835-43. [PMID: 1420196 DOI: 10.1021/bi00159a026] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The 51-kDa telomere protein from Euplotes crassus binds to the extreme terminus of macronuclear telomeres, generating a very salt-stable telomeric DNA-protein complex. The protein recognizes both the sequence and the structure of the telomeric DNA. To explore how the telomere protein recognizes and binds telomeric DNA, we have examined the DNA-binding specificity of the purified protein using oligonucleotides that mimic natural and mutant versions of Euplotes telomeres. The protein binds very specifically to the 3' terminus of single-stranded oligonucleotides with the sequence (T4G4) > or = 3 T4G2; even slight modifications to this sequence reduce binding dramatically. The protein does not bind oligonucleotides corresponding to the complementary C4A4 strand of the telomere or to double-stranded C4A4.T4G4-containing sequences. Digestion of the telomere protein with trypsin generates an N-terminal protease-resistant fragment of approximately 35 kDa. This 35-kDa peptide appears to comprise the DNA-binding domain of the telomere protein as it retains most of the DNA-binding characteristics of the native 51-kDa protein. For example, the 35-kDa peptide remains bound to telomeric DNA in 2 M KCl. Additionally, the peptide binds well to single-stranded oligonucleotides that have the same sequence as the T4G4 strand of native telomeres but binds very poorly to mutant telomeric DNA sequences and double-stranded telomeric DNA. Removal of the C-terminal 15 kDa from the telomere protein does diminish the ability of the protein to bind only to the terminus of a telomeric DNA molecule.
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Affiliation(s)
- C M Price
- Department of Chemistry, University of Nebraska, Lincoln 68588
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36
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The yeast alpha 1 and MCM1 proteins bind a single strand of their duplex DNA recognition site. Mol Cell Biol 1992. [PMID: 1630462 DOI: 10.1128/mcb.12.8.3573] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The yeast cell type regulator alpha 1 cooperates with a constitutive factor, MCM1 protein, to recognize the promoter and activate transcription of several alpha-specific genes. I show here that the alpha 1 and MCM1 proteins bind specifically to one of the two strands of their recognition sequence. This single-strand-binding activity shares several characteristics with the duplex-binding properties of these proteins: (i) the MCM1 protein binds alone to single-stranded and duplex sequences of both the alpha-specific (P'Q) and a-specific (P) binding sites; (ii) the alpha 1 protein requires both the MCM1 protein and the Q sequence to bind either single-stranded or duplex DNA; (iii) the alpha 1 protein stimulates binding of the MCM1 protein to both single-stranded and duplex DNAs; and (iv) the affinities of the proteins for single-stranded and duplex DNAs are comparable.
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37
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Grayhack EJ. The yeast alpha 1 and MCM1 proteins bind a single strand of their duplex DNA recognition site. Mol Cell Biol 1992; 12:3573-82. [PMID: 1630462 PMCID: PMC364623 DOI: 10.1128/mcb.12.8.3573-3582.1992] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
The yeast cell type regulator alpha 1 cooperates with a constitutive factor, MCM1 protein, to recognize the promoter and activate transcription of several alpha-specific genes. I show here that the alpha 1 and MCM1 proteins bind specifically to one of the two strands of their recognition sequence. This single-strand-binding activity shares several characteristics with the duplex-binding properties of these proteins: (i) the MCM1 protein binds alone to single-stranded and duplex sequences of both the alpha-specific (P'Q) and a-specific (P) binding sites; (ii) the alpha 1 protein requires both the MCM1 protein and the Q sequence to bind either single-stranded or duplex DNA; (iii) the alpha 1 protein stimulates binding of the MCM1 protein to both single-stranded and duplex DNAs; and (iv) the affinities of the proteins for single-stranded and duplex DNAs are comparable.
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Affiliation(s)
- E J Grayhack
- Department of Biology, University of Rochester, New York 14627
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38
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Gualberto A, Patrick RM, Walsh K. Nucleic acid specificity of a vertebrate telomere-binding protein: evidence for G-G base pair recognition at the core-binding site. Genes Dev 1992; 6:815-24. [PMID: 1577275 DOI: 10.1101/gad.6.5.815] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
A factor from avian cells formed complexes with telomeric sequences and other single-stranded probes that contained tracts of guanine residues. Nucleoprotein complexes with telomere probes required two or more of the telomeric repeats that were incapable of Watson-Crick base-pairing. Methylation interference and protection experiments identified guanine N7 residues that were critical for the formation of the nucleoprotein complex and for the formation of a higher-order structure that occurred in the absence of the protein. Substitutions of deoxyinosine (dI) for deoxyguanosine (dG) demonstrated that the exocyclic N2 amino groups in the internal telomeric repeat, but not the terminal repeat, were required for the formation of the chemically protected structure and for protein binding. On the basis of these data we propose that the factor specifically recognizes a hairpin DNA structure that is stabilized by intramolecular G-G base-pairing between the telomere repeats. The positions of the critical guanine N2 and N7 groups indicate a G-G base-pairing configuration, where guanines function as hydrogen bond donors at the internal telomeric repeat and hydrogen bond acceptors at the terminal telomeric repeat.
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Affiliation(s)
- A Gualberto
- Department of Physiology and Biophysics, Case Western Reserve University, Cleveland, Ohio 44106
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39
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Jansen-Dürr P, Boshart M, Lupp B, Bosserhoff A, Frank RW, Schütz G. The rat poly pyrimidine tract binding protein (PTB) interacts with a single-stranded DNA motif in a liver-specific enhancer. Nucleic Acids Res 1992; 20:1243-9. [PMID: 1561080 PMCID: PMC312165 DOI: 10.1093/nar/20.6.1243] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
We characterized and purified a protein from rat liver which specifically binds to a DNA motif present in a liver-specific enhancer of the rat tyrosine aminotransferase (TAT) gene, when offered as single-stranded DNA. Binding is highly sequence-specific and coincides with a region known to be essential for function of the enhancer. Microsequencing revealed that this protein is the rat homologue of the mouse and human poly Pyrimidine Tract binding protein (PTB), which has been shown to bind to premRNA and may participate in RNA splicing. This finding was corroborated by subsequent Western blot experiments using a PTB-specific antibody. These findings indicate a possible dual role for this protein in RNA processing and transcription.
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Affiliation(s)
- P Jansen-Dürr
- Institute of Cell and Tumor Biology, German Cancer Research Center, Heidelberg
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40
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Fourcade-Peronnet F, Codani-Simonart S, Best-Belpomme M. A nuclear single-stranded-DNA binding factor interacts with the long terminal repeats of the 1731 Drosophila retrotransposon. J Virol 1992; 66:1682-7. [PMID: 1371170 PMCID: PMC240910 DOI: 10.1128/jvi.66.3.1682-1687.1992] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Using gel mobility assays, we have detected two proteins that bind in the U3 region of the 1731 retrotransposon long terminal repeats (between positions -110 and -73) in nuclear extracts from Drosophila melanogaster cultured cells. The first one binds double-stranded DNA, whereas the other binds the mRNA-like strand in a sequence-specific manner. We report here the characterization of the latter protein, named NssBF for nuclear single-stranded-DNA binding factor. Gel filtration shows an apparent molecular mass of 95 kDa for NssBF. The points of contact between NssBF and its single-stranded DNA target were determined. This protein binds neither the complementary strand nor the corresponding RNA sequence. A possible role of NssBF in transcription is discussed.
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Affiliation(s)
- F Fourcade-Peronnet
- URA Centre National de la Recherche Scientifique 1135, Université Pierre et Marie Curie, Paris, France
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41
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Stark HC, Weinberger O, Weinberger J. Common double- and single-stranded DNA binding factor for a sterol regulatory element. Proc Natl Acad Sci U S A 1992; 89:2180-4. [PMID: 1549579 PMCID: PMC48620 DOI: 10.1073/pnas.89.6.2180] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
A cis-acting element necessary for sterol regulation, SRE-1, has previously been identified in the promoters of the low density lipoprotein receptor, hydroxymethylglutaryl (HMG)-CoA reductase, and HMG-CoA synthase genes. In this report we describe a nuclear factor, SRE-BF, isolated from Chinese hamster ovary nuclear extracts, that binds to the SRE-1 octanucleotide sequence. In addition to sequence-specific binding to SRE-1, as indicated by competition analysis with double-stranded DNA fragments, single-stranded oligomer DNA sequences also compete for binding in a sequence-specific fashion. Photochemical cross-linking experiments suggest that a common protein factor, with apparent molecular mass of 45-49 kDa, recognizes both single-stranded and double-stranded SRE-1. The binding specificity of SRE-BF to single-stranded SRE-1 closely correlates with the reported in vivo ability of SRE-1 to direct sterol responsiveness of transcription.
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Affiliation(s)
- H C Stark
- Department of Medicine, Columbia University, New York, NY 10032
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42
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Spitkovsky DD, Royer-Pokora B, Delius H, Kisseljov F, Jenkins NA, Gilbert DJ, Copeland NG, Royer HD. Tissue restricted expression and chromosomal localization of the YB-1 gene encoding a 42 kD nuclear CCAAT binding protein. Nucleic Acids Res 1992; 20:797-803. [PMID: 1542575 PMCID: PMC312020 DOI: 10.1093/nar/20.4.797] [Citation(s) in RCA: 42] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
YB-1 cDNA clones were isolated by binding site screening of a Hela expression library using a human papillomavirus type 18 enhancer oligonucleotide. YB-1 belongs to a family of transcription factors which bind to recognition sequences containing a core CCAAT element. YB-1 bound to its single stranded recognition sequence on the sense strand but not to the anti-sense strand. A synthetic peptide antiserum derived from the predicted YB-1 amino acid sequence identified a 42 kD nuclear protein in immunoblots. A protein with the same size was detected by binding site blotting experiments using the HPV18 enhancer oligonucleotide which bound YB-1. YB-1 gene expression was restricted in tissues from a human 24 week old fetus. High levels of YB-1 mRNA were present in heart, muscle, liver, lung, adrenal gland and the brain, in contrast, low amounts of YB-1 mRNA were found in thymus, kidney, bone marrow and spleen. In pancreas, bladder, stomach and testis YB-1 mRNA could not be detected by Northern hybridization. Finally, we have identified four YB-1 related loci in the mouse genome and have mapped these loci to four different mouse chromosomes by interspecific backcross analysis.
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Affiliation(s)
- D D Spitkovsky
- Angewandte Tumorvirologie, Deutsches Krebsforschungszentrum, Heidelberg, FRG
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43
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Rejman J, Landers J, Goldberger A, McCormick DJ, Gosse B, Spelsberg TC. Purification of a nuclear protein (receptor binding factor-1) associated with the chromatin acceptor sites for the avian oviduct progesterone receptor. JOURNAL OF PROTEIN CHEMISTRY 1991; 10:651-67. [PMID: 1815590 DOI: 10.1007/bf01025717] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The specific high affinity binding of the avian oviduct progesterone receptor (PR) to target cell nuclei and chromatin has been shown to involve DNA complexed with specific chromatin acceptor proteins. One of these chromatin acceptor proteins has been partially purified and found to be a small hydrophobic protein with a broad pI of 5.0-6.0 [Goldberger and Spelsberg (1988), Biochem. 27, 2103-2109]. Using western immunoblots with anti-RBF-1 polyclonal antibodies to monitor the purification, a 10 kD candidate acceptor protein, termed the Receptor Binding Factor-1 (RBF-1), has been purified to apparent homogeneity. RBF-1 has an amino acid composition consistent with a hydrophobic protein having an acidic pI and a unique N-terminal sequence. Two-dimensional polyacrylamide gel electrophoresis and high-performance capillary electrophoresis support the purity of a protein congruent to 10 kD in size, having an acidic pI, but with evidence of several differently charged isoforms. Phosphatase treatment provides evidence that charge heterogeneity may result from variable phosphorylation states. A role of this factor as a candidate "acceptor protein" in the chromatin acceptor sites for the avian oviduct PR is proposed.
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Affiliation(s)
- J Rejman
- SYVA Corp., Palo Alto, California 94303
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44
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Murdoch FE, Grunwald KA, Gorski J. Marked effects of salt on estrogen receptor binding to DNA: biologically relevant discrimination between DNA sequences. Biochemistry 1991; 30:10838-44. [PMID: 1932006 DOI: 10.1021/bi00109a005] [Citation(s) in RCA: 31] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Avidin-biotin complexed with DNA (ABCD) assays were employed to determine the binding affinity of estrogen receptor (ER) to DNA under various salt conditions. Type and concentration of salt in the reaction buffer dramatically affected the ability of the ER to discriminate between DNA sequences. Under appropriate salt conditions, ER was able to bind to the estrogen response element from the Xenopus vitellogenin A2 gene with at least 3 orders of magnitude greater affinity than a two base pair mutant sequence, and 5 orders of magnitude greater affinity than plasmid DNA. In these studies, the best discrimination was observed under conditions of salt type and concentration that more closely approximated intracellular conditions, i.e., 100-150 mM potassium salts. Analysis of the binding affinities for ER to all three types of DNA over a range of KCl concentrations indicated that the ionic interactions upon ER binding were the same for the three DNA molecules tested. Therefore, the additional stability of ER binding to target DNA sequences was contributed by nonionic interactions.
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Affiliation(s)
- F E Murdoch
- Department of Biochemistry, University of Wisconsin, Madison 53706
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45
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Liu ES, Lee AS. Common sets of nuclear factors binding to the conserved promoter sequence motif of two coordinately regulated ER protein genes, GRP78 and GRP94. Nucleic Acids Res 1991; 19:5425-31. [PMID: 1923827 PMCID: PMC328908 DOI: 10.1093/nar/19.19.5425] [Citation(s) in RCA: 60] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
The GRP78 and GRP94 are two constitutively expressed ER resident proteins that are coordinately induced in response to stress conditions. The control of their induction is at the transcriptional level. We have previously demonstrated that the GRP78 and the GRP94 promoters share a common regulatory domain which is highly conserved. We report here that within this 36 bp promoter region is a CG/CAAT and a GC-rich sequence motif which are important for basal level and induced expression of the gene. Gel mobility shift assays with HeLa nuclear extracts and the conserved element from GRP78 and GRP94 show two shared, specific protein-DNA complexes. By ultraviolet cross-linking, the sizes of the proteins labeled in the slower-migrating complex are 210-, 110-, a doublet at 90/92- and 70 kD, and in the faster-migrating complex, protein species of about 55 kD. The formation of the second complex can be inhibited by competition with the coding strand of the conserved GRP element in a sequence specific manner. In addition, the Ku autoantigen which is abundant in HeLa cell extracts also binds. The sizes of the nuclear factors binding to the GRP78 and GRP94 conserved promoter elements are strikingly similar, providing further evidence that the two genes are coordinately regulated by common trans-acting factors.
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Affiliation(s)
- E S Liu
- Department of Biochemistry, University of Southern California School of Medicine, Los Angeles 90033
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46
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Finocchiaro LM, Amati P, Glikin GC. Single strand binding protein specific for the polyoma early-coding strand of PEA1 (AP1) regulatory sequence. Nucleic Acids Res 1991; 19:4279-87. [PMID: 1651484 PMCID: PMC328574 DOI: 10.1093/nar/19.15.4279] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
We have shown that nuclear and cytosolic proteins from embryonal carcinoma F9 cells are able to bind to the early-coding strand of polyoma enhancer A domain. As demonstrated by mobility shift specific competition experiments, DNase I footprinting, depurination and depyrimidation interference, and proteolytic clipping performed with single stranded oligonucleotides, some of these proteins bind specifically to the early-coding PEA1 (AP1) motif. In addition, 'Southwestern' analysis has made possible the identification of a 46 KD nuclear protein that binds to this sequence. These cellular proteins did not bind to the complementary single strand as demonstrated by mobility shift analysis, nor did they bind to RNA synthesized in vitro by using the complementary strand as template. They were also shown to be different from their corresponding double strand binding factors. This new dimension in the functional flexibility and complexity of the polyoma enhancer suggests new properties of the classic regulating sequences that could provide additional modulation of regulating activities.
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Affiliation(s)
- L M Finocchiaro
- Dipartimento di Biopatologia Umana, Università La Sapienza, Rome, Italy
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47
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Identification of single-stranded-DNA-binding proteins that interact with muscle gene elements. Mol Cell Biol 1991. [PMID: 2005890 DOI: 10.1128/mcb.11.4.1944] [Citation(s) in RCA: 41] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A sequence-specific DNA-binding protein from skeletal-muscle extracts that binds to probes of three muscle gene DNA elements is identified. This protein, referred to as muscle factor 3, forms the predominant nucleoprotein complex with the MCAT gene sequence motif in an electrophoretic mobility shift assay. This protein also binds to the skeletal actin muscle regulatory element, which contains the conserved CArG motif, and to a creatine kinase enhancer probe, which contains the E-box motif, a MyoD-binding site. Muscle factor 3 has a potent sequence-specific, single-stranded-DNA-binding activity. The specificity of this interaction was demonstrated by sequence-specific competition and by mutations that diminished or eliminated detectable complex formation. MyoD, a myogenic determination factor that is distinct from muscle factor 3, also bound to single-stranded-DNA probes in a sequence-specific manner, but other transcription factors did not. Multiple copies of the MCAT motif activated the expression of a heterologous promoter, and a mutation that eliminated expression was correlated with diminished factor binding. Muscle factor 3 and MyoD may be members of a class of DNA-binding proteins that modulate gene expression by their abilities to recognize DNA with unusual secondary structure in addition to specific sequence.
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48
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Abstract
We used chloramphenicol acetyltransferase (CAT) assays to identify and characterize cis-acting elements responsible for rat neu promoter function. Deletion of a region of the neu promoter (-504 to -312) resulted in a marked decrease in CAT activity, indicating that this promoter region corresponds to a positive cis-acting element. Using band shift assays and methylation interference analyses, we further identified a specific protein-binding sequence, AAGATAAAACC (-466 to -456), that binds a specific trans-acting factor termed RVF (for EcoRV factor on the neu promoter). The RVF-binding site is required for maximum transcriptional activity of the rat neu promoter. This same sequence is also found in the corresponding regions of both human and mouse neu promoters. Furthermore, this sequence can enhance the CAT activity driven by a minimum promoter of the thymidine kinase gene in an orientation-independent manner, and thus it behaves as an enhancer. Our results demonstrate that RVF is the major DNA-binding protein contributing to enhancer activity. In addition, Southwestern (DNA-protein) blot analysis using the RVF-binding site as a probe points to a 60-kDa polypeptide as a potential candidate for RVF.
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49
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Santoro IM, Yi TM, Walsh K. Identification of single-stranded-DNA-binding proteins that interact with muscle gene elements. Mol Cell Biol 1991; 11:1944-53. [PMID: 2005890 PMCID: PMC359879 DOI: 10.1128/mcb.11.4.1944-1953.1991] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
A sequence-specific DNA-binding protein from skeletal-muscle extracts that binds to probes of three muscle gene DNA elements is identified. This protein, referred to as muscle factor 3, forms the predominant nucleoprotein complex with the MCAT gene sequence motif in an electrophoretic mobility shift assay. This protein also binds to the skeletal actin muscle regulatory element, which contains the conserved CArG motif, and to a creatine kinase enhancer probe, which contains the E-box motif, a MyoD-binding site. Muscle factor 3 has a potent sequence-specific, single-stranded-DNA-binding activity. The specificity of this interaction was demonstrated by sequence-specific competition and by mutations that diminished or eliminated detectable complex formation. MyoD, a myogenic determination factor that is distinct from muscle factor 3, also bound to single-stranded-DNA probes in a sequence-specific manner, but other transcription factors did not. Multiple copies of the MCAT motif activated the expression of a heterologous promoter, and a mutation that eliminated expression was correlated with diminished factor binding. Muscle factor 3 and MyoD may be members of a class of DNA-binding proteins that modulate gene expression by their abilities to recognize DNA with unusual secondary structure in addition to specific sequence.
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Affiliation(s)
- I M Santoro
- Department of Physiology and Biophysics, Case Western Reserve University, Cleveland, Ohio 44106
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50
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Abstract
We used chloramphenicol acetyltransferase (CAT) assays to identify and characterize cis-acting elements responsible for rat neu promoter function. Deletion of a region of the neu promoter (-504 to -312) resulted in a marked decrease in CAT activity, indicating that this promoter region corresponds to a positive cis-acting element. Using band shift assays and methylation interference analyses, we further identified a specific protein-binding sequence, AAGATAAAACC (-466 to -456), that binds a specific trans-acting factor termed RVF (for EcoRV factor on the neu promoter). The RVF-binding site is required for maximum transcriptional activity of the rat neu promoter. This same sequence is also found in the corresponding regions of both human and mouse neu promoters. Furthermore, this sequence can enhance the CAT activity driven by a minimum promoter of the thymidine kinase gene in an orientation-independent manner, and thus it behaves as an enhancer. Our results demonstrate that RVF is the major DNA-binding protein contributing to enhancer activity. In addition, Southwestern (DNA-protein) blot analysis using the RVF-binding site as a probe points to a 60-kDa polypeptide as a potential candidate for RVF.
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Affiliation(s)
- D H Yan
- Department of Tumor Biology, University of Texas, M.D. Anderson Cancer Center, Houston 77030
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