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Desrivières S, Kuhn K, Müller J, Gläser M, Laria NCP, Korder J, Sonnentag M, Neumann T, Schwarz J, Schäfer J, Hamon C, Groner B, Prinz T. Comparison of the nuclear proteomes of mammary epithelial cells at different stages of functional differentiation. Proteomics 2007; 7:2019-37. [PMID: 17514683 DOI: 10.1002/pmic.200600994] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
The progression of stem cells to proliferating progenitor cells and finally to a quiescent differentiated state is a hallmark of organ development. This process proceeds through distinct steps and is regulated through cell-cell interactions and by systemically and locally acting factors. We have established a cell culture system which recapitulates features of mammary gland development in vitro and allows the comparison of three characteristic differentiation stages. Cell fate decisions relating to proliferation and differentiation are dependent on the function of proteins in the nucleus. Therefore, we have applied proteomic approaches, including 1- and 2-DE coupled with MS and a gel-free system, called protein sequence tag technology (PST), to assess the changes in the nuclear protein composition during differentiation of mammary epithelial cells. We identified about 250 individual proteins which are present in the nucleus of proliferating and functionally differentiated mammary epithelial cells. We functionally categorised the differentially expressed proteins and identified a multitude of proteins that regulate gene expression at the transcriptional or post-transcriptional level. This analysis greatly enriches our global view of the dynamic changes of nuclear proteins during the development of mammary epithelial cells and suggests models for the control of differentiation-specific protein expression.
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Kuhn K, Prinz T, Schäfer J, Baumann C, Schärfke M, Kienle S, Schwarz J, Steiner S, Hamon C. Protein sequence tags: A novel solution for comparative proteomics. Proteomics 2005; 5:2364-8. [PMID: 15887190 DOI: 10.1002/pmic.200401306] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Comparative proteome profiling using stable isotope peptide labelling and mass spectrometry has emerged as a promising strategy. Here, we show the broad potential of our proprietary protein sequence tag (PST) technology. A special feature of PST is its ability to detect a wide variety of proteins including the pharmaceutically relevant membrane and nuclear proteins. This procedure addresses a similar number of proteins, compared to the multidimensional protein identification technology approach, but offers additionally a quantitative analysis with its recently developed quantitative PST version.
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Affiliation(s)
- Karsten Kuhn
- Proteome Sciences R&D, Frankfurt am Main, Germany
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3
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Janke J, Schlüter K, Jandrig B, Theile M, Kölble K, Arnold W, Grinstein E, Schwartz A, Estevéz-Schwarz L, Schlag PM, Jockusch BM, Scherneck S. Suppression of tumorigenicity in breast cancer cells by the microfilament protein profilin 1. J Exp Med 2000; 191:1675-1686. [PMID: 10811861 PMCID: PMC2193149 DOI: 10.1084/jem.191.10.1675] [Citation(s) in RCA: 113] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/1999] [Accepted: 02/23/2000] [Indexed: 01/10/2023] Open
Abstract
Differential display screening was used to reveal differential gene expression between the tumorigenic breast cancer cell line CAL51 and nontumorigenic microcell hybrids obtained after transfer of human chromosome 17 into CAL51. The human profilin 1 (PFN1) gene was found overexpressed in the microcell hybrid clones compared with the parental line, which displayed a low profilin 1 level. A comparison between several different tumorigenic breast cancer cell lines with nontumorigenic lines showed consistently lower profilin 1 levels in the tumor cells. Transfection of PFN1 cDNA into CAL51 cells raised the profilin 1 level, had a prominent effect on cell growth, cytoskeletal organization and spreading, and suppressed tumorigenicity of the stable, PFN1-overexpressing cell clones in nude mice. Immunohistochemical analysis revealed intermediate and low levels of profilin 1 in different human breast cancers. These results suggest profilin 1 as a suppressor of the tumorigenic phenotype of breast cancer cells.
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Affiliation(s)
- Jürgen Janke
- Department of Medical Genetics, Max-Delbrück-Center for Molecular Medicine, 13092 Berlin-Buch, Germany
| | - Kathrin Schlüter
- Department of Cell Biology, Zoological Institute, Technical University of Braunschweig, 38106 Braunschweig, Germany
| | - Burkhard Jandrig
- Department of Medical Genetics, Max-Delbrück-Center for Molecular Medicine, 13092 Berlin-Buch, Germany
| | - Michael Theile
- Department of Medical Genetics, Max-Delbrück-Center for Molecular Medicine, 13092 Berlin-Buch, Germany
| | - Konrad Kölble
- Institute of Pathology, Charité Hospital, Humboldt University, 10117 Berlin, Germany
- Clinic of Surgery and Surgical Oncology, Robert Roessle Hospital, 13122 Berlin-Buch, Germany
| | | | - Edgar Grinstein
- Department of Medical Genetics, Max-Delbrück-Center for Molecular Medicine, 13092 Berlin-Buch, Germany
| | - Arnfried Schwartz
- Department of Medical Genetics, Max-Delbrück-Center for Molecular Medicine, 13092 Berlin-Buch, Germany
| | - Lope Estevéz-Schwarz
- Clinic of Surgery and Surgical Oncology, Robert Roessle Hospital, 13122 Berlin-Buch, Germany
| | - Peter M. Schlag
- Clinic of Surgery and Surgical Oncology, Robert Roessle Hospital, 13122 Berlin-Buch, Germany
| | - Brigitte M. Jockusch
- Department of Cell Biology, Zoological Institute, Technical University of Braunschweig, 38106 Braunschweig, Germany
| | - Siegfried Scherneck
- Department of Medical Genetics, Max-Delbrück-Center for Molecular Medicine, 13092 Berlin-Buch, Germany
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4
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Kimura K, Saga H, Hayashi K, Obata H, Chimori Y, Ariga H, Sobue K. c-Myc gene single-strand binding protein-1, MSSP-1, suppresses transcription of alpha-smooth muscle actin gene in chicken visceral smooth muscle cells. Nucleic Acids Res 1998; 26:2420-5. [PMID: 9580695 PMCID: PMC147545 DOI: 10.1093/nar/26.10.2420] [Citation(s) in RCA: 25] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
The expression of alpha-smooth muscle actin is coordinately regulated by positive and negative cis- elements in the promoter region. Although cis -elements and trans -acting factors involved in the positive regulation of the alpha-smooth muscle (alpha-SM) actin gene have been well characterized, details of negative regulation remain unclear. In functional analyses using cultured gizzard smooth muscle cells, we identified a sequence ranging from -238 to -219 in the promoter region as a novel negative element. Mutation and deletion analyses further revealed that a sequence, TATCTTA (-228 to -222), is essential for negative regulation. Gel shift assay and Southwestern blotting indicated that a nuclear protein factor specifically interacts with single- or double-strand DNA including this sequence, and the protein factor displays a highly potent binding to the sense strand DNA. cDNA cloning and gel shift analysis using anti-MSSP-1 antibodies revealed that this protein factor is a chicken homolog of human MSSP-1 (c- myc gene single-strand binding protein-1). In fact, overexpression of MSSP-1 in cultured smooth muscle cells suppresses the promoter activity. These results suggest a novel function of MSSP-1 regarding the transcriptional regulation of alpha-sm actin gene.
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Affiliation(s)
- K Kimura
- Department of Neurochemistry and Neuropharmacology, Biomedical Research Center, Osaka University Medical School, 2-2 Yamadaoka, Suita, Osaka 565, Japan
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5
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Momiyama T, Hayashi K, Obata H, Chimori Y, Nishida T, Ito T, Kamiike W, Matsuda H, Sobue K. Functional involvement of serum response factor in the transcriptional regulation of caldesmon gene. Biochem Biophys Res Commun 1998; 242:429-35. [PMID: 9446812 DOI: 10.1006/bbrc.1997.7959] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
A 22-bp fragment including the CArG element (CArG1) is essential for the transcription of the caldesmon gene. In this study, we investigated the effects of serum response factor (SRF) on the functional regulation of caldesmon promoter in smooth muscle cells. Gel supershift assay revealed that SRF was one component of the CArG1-protein complex. Dominant-negative mutants of SRF suppressed the promoter activity of caldesmon, whereas wild-type SRF overcame this suppression. These results suggest that SRF functions as a core activating factor of the caldesmon promoter. Furthermore, fractionation of smooth muscle cells' nuclear extracts using DNA affinity paramagnetic particles suggests that SRF transactivates the caldesmon promoter in concert with additional factors in the flow-through fraction recruited to the CArG element.
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Affiliation(s)
- T Momiyama
- Department of Neurochemistry and Neuropharmacology, Biomedical Research Center, Osaka University Medical School, Japan
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6
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Kelm RJ, Elder PK, Strauch AR, Getz MJ. Sequence of cDNAs encoding components of vascular actin single-stranded DNA-binding factor 2 establish identity to Puralpha and Purbeta. J Biol Chem 1997; 272:26727-33. [PMID: 9334258 DOI: 10.1074/jbc.272.42.26727] [Citation(s) in RCA: 82] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Transcriptional repression of the mouse vascular smooth muscle alpha-actin gene in fibroblasts and myoblasts is mediated, in part, by the interaction of two single-stranded DNA binding activities with opposite strands of an essential transcription enhancer factor-1 recognition element (Sun, S., Stoflet, E. S., Cogan, J. G., Strauch, A. R., and Getz, M. J. (1995) Mol. Cell. Biol. 15, 2429-2436). One of these activities, previously designated vascular actin single-stranded DNA-binding factor 2 includes two distinct polypeptides (p44 and p46) which specifically interact with the purine-rich strand of both the enhancer and a related element in a protein coding exon of the gene (Kelm, R. J., Jr., Sun, S., Strauch, A. R., and Getz, M. J. (1996) J. Biol. Chem. 271, 24278-24285). Expression screening of a mouse lung cDNA library with a vascular actin single-stranded DNA-binding factor 2 recognition element has now resulted in the isolation of two distinct cDNA clones that encode p46 and p44. One of these proteins is identical to Puralpha, a retinoblastoma-binding protein previously implicated in both transcriptional activation and DNA replication. The other is a related family member, presumably Purbeta. Comparative band shift and Southwestern blot analyses conducted with cellular p46, p44, and cloned Pur proteins synthesized in vitro and in vivo, establish identity of p46 with Puralpha and p44 with Purbeta. This study implicates Puralpha and/or Purbeta in the control of vascular smooth muscle alpha-actin gene transcription.
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Affiliation(s)
- R J Kelm
- Department of Biochemistry and Molecular Biology, Mayo Clinic/Foundation, Rochester, Minnesota 55905, USA
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7
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Obata H, Hayashi K, Nishida W, Momiyama T, Uchida A, Ochi T, Sobue K. Smooth muscle cell phenotype-dependent transcriptional regulation of the alpha1 integrin gene. J Biol Chem 1997; 272:26643-51. [PMID: 9334246 DOI: 10.1074/jbc.272.42.26643] [Citation(s) in RCA: 48] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
The expressional regulation of chicken alpha1 integrin in smooth muscle cells was studied. The alpha1 integrin mRNA was expressed developmentally and was distributed dominantly in vascular and visceral smooth muscles in chick embryos. In a primary culture of smooth muscle cells, alpha1 integrin expression was dramatically down-regulated during serum-induced dedifferentiation. Promoter analyses revealed that the 5'-upstream region (-516 to +281) was sufficient for transcriptional activation in differentiated smooth muscle cells but not in dedifferentiated smooth muscle cells or chick embryo fibroblasts. Like other alpha integrin promoters, the promoter region of the alpha1 integrin gene lacks TATA and CCAAT boxes and contains binding sites for AP1 and AP2. The essential difference from other alpha integrin promoters is the presence of a CArG box-like motif. Deletion and site-directed mutation analyses revealed that the CArG box-like motif was an essential cis-element for transcriptional activation in differentiated smooth muscle cells, whereas the binding sites for AP1 and AP2 were not. Using specific antibodies, a nuclear protein factor specifically bound to the CArG box-like motif was identified as serum response factor. These results indicate that alpha1 integrin expression in smooth muscle cells is regulated transcriptionally in a phenotype-dependent manner and that serum response factor binding plays a crucial role in this regulation.
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Affiliation(s)
- H Obata
- Department of Neurochemistry and Neuropharmacology, Biomedical Research Center, Japan
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8
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Grinstein E, Weinert I, Droese B, Pagano M, Royer HD. Cell cycle regulation of nuclear factor p32 DNA-binding activity by novel phase-specific inhibitors. J Biol Chem 1996; 271:9215-9222. [PMID: 8621580 DOI: 10.1074/jbc.271.16.9215] [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: 01/31/2023] Open
Abstract
The nuclear factor p92, originally discovered by its interaction with the human papillomavirus type 18 enhancer, is a cellular protein whose activity is restricted to S phase in human primary fibroblasts. The human papillomavirus type 18 p92 binding sequence confers enhancer activity on a heterologous promoter, suggesting that p92 acts as a transcription factor. We have identified a class of nuclear inhibitory proteins, I-92s, which noncovalently associate with p92 but not with other transcription factors such as AP1, E2F, or NF-kappaB. Different I-92s occur in G1, G2, and G0, while no I-92 is detectable in S phase. Phase-specific inhibitors, therefore, are responsible for the cell cycle dependence of p92 activity and provide a novel mechanism linking transcription factor regulation with the cell cycle.
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Affiliation(s)
- E Grinstein
- Department of Medical Genetics, Max-Delbrück Center for Molecular Medicine, Berlin, Germany
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9
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Yano H, Hayashi K, Momiyama T, Saga H, Haruna M, Sobue K. Transcriptional regulation of the chicken caldesmon gene. Activation of gizzard-type caldesmon promoter requires a CArG box-like motif. J Biol Chem 1995; 270:23661-6. [PMID: 7559534 DOI: 10.1074/jbc.270.40.23661] [Citation(s) in RCA: 45] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Caldesmon, which plays a vital role in the actomyosin system, is distributed in smooth muscle and non-muscle cells, and its isoformal interconversion between a high M(r) form and low M(r) form is a favorable molecular event for studying phenotypic modulation of smooth muscle cells. Genomic analysis reveals two promoters, of which the gizzard-type promoter displays much higher activity than the brain-type promoter. Here, we have characterized transcriptional regulation of the gizzard-type promoter. Transient transfection assays in chick gizzard smooth muscle cells, chick embryo fibroblasts, mouse skeletal muscle cell line (C2C12), and HeLa cells revealed that the promoter activity was high in smooth muscle cells and fibroblasts, but was extremely low in other cells. Cell type-specific promoter activity depended on an element, CArG1, containing a unique CArG box-like motif (CCAAAAAAGG) at -315, while multiple E boxes were not directly involved in this event. Gel shift assays showed the specific interaction between the CArG1 and nuclear protein factors in smooth muscle cells and fibroblasts. These results suggest that the CArG1 is an essential cis-element for cell type-specific expression of caldesmon and that the function of CArG1 might be controlled under phenotypic modulation of smooth muscle cells.
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Affiliation(s)
- H Yano
- Department of Neurochemistry and Neuropharmacology, Osaka University Medical School, Japan
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10
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Szabó P, Moitra J, Rencendorj A, Rákhely G, Rauch T, Kiss I. Identification of a nuclear factor-I family protein-binding site in the silencer region of the cartilage matrix protein gene. J Biol Chem 1995; 270:10212-21. [PMID: 7730325 DOI: 10.1074/jbc.270.17.10212] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Cartilage matrix protein (CMP) is synthesized by chondrocytes in a developmentally regulated manner. Here we have dissected promoter upstream elements involved in its transcriptional regulation. We show that although the 79-base pair CMP minimal promoter is promiscuous, 1137 base pairs of 5'-flanking region are capable of directing tissue- and developmental stage-specific transcription when fused to a reporter gene. This results from two positive control regions which, in proliferating chondrocytes, relieve the repression mediated by two non-tissue-specific negative control regions. Characterization of the promoter proximal silencer by DNase I footprinting and gel shifts revealed the presence of two elements, SI and SII, which bound mesenchymal cell proteins. Methylation interference analysis indicated a gapped palindromic binding site similar to nuclear factor I (NF-I) family proteins within SI, but only a half-site within SII. Gel shift assays with specific NF-I and mutated SI competitors, binding of recombinant NF-I, as well as supershift analysis with NF-I-specific antiserum verified the binding of NF-I family proteins to the SI element. Double-stranded SI and SII oligonucleotides inserted in single copy in either orientation were found to repress both homologous and heterologous promoters upon transfection into mesenchymal cells. Transcriptional repression also occurred when a consensus NF-I site itself was fused to the CMP minimal promoter. We conclude that NF-I-related protein(s) can mediate transcriptional repression in cells of mesenchymal origin.
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Affiliation(s)
- P Szabó
- Institute of Biochemistry, Hungarian Academy of Sciences, Szeged
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11
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Affiliation(s)
- A Ruddell
- Department of Microbiology and Immunology, University of Rochester, New York 14642
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12
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Hann SR. Methionine deprivation regulates the translation of functionally-distinct c-Myc proteins. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 1995; 375:107-16. [PMID: 7645422 DOI: 10.1007/978-1-4899-0949-7_10] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Numerous studies have demonstrated a critical role for the c-myc gene in the control of cellular growth. Alterations of the c-myc gene have been found associated with many different types of tumors in several species, including humans. The increased synthesis of one of the major forms of c-Myc protein, c-Myc 1, upon methionine deprivation provides a link between the regulation of oncogenes and the nutritional status of the cell. While deregulation or overexpression of the other major form, c-Myc 2, has been shown to cause tumorigenesis, the synthesis of c-Myc 1 protein is lost in many tumors. This suggests that the c-Myc 1 protein is necessary to keep the c-Myc 2 protein "in check" and prevent certain cells from becoming tumorigenic. Indeed, we have shown that overproduction of c-Myc 1 can inhibit cell growth. We have also shown that c-Myc 1 and 2 proteins have a differential molecular function in the regulation of transcription through a new binding site of Myc/Max heterodimers. We have also recently identified new translational forms of the c-Myc protein which we term delta-c-Myc. These proteins arise from translational initiation at downstream start sites which yield N-terminally-truncated c-Myc proteins. Since these proteins lack a significant portion of the transactivation domain of c-Myc, they behave as dominant-negative inhibitors of the full-length c-Myc 1 and 2 proteins. The synthesis of delta-c-Myc proteins is also regulated during cell growth and is repressed by methionine deprivation. Therefore, the synthesis of c-Myc 1 and delta-c-Myc proteins are reciprocally regulated by methionine availability. We have also found some tumor cell lines which synthesize high levels of the delta-c-Myc proteins. Taken together, our data suggest that c-Myc function is dependent on the levels of these different translational forms of c-Myc protein which are regulated by the nutritional status of the cell during growth. Numerous reports have demonstrated a fundamental and diverse role for the myc gene in cellular events, including proliferation, differentiation and apoptosis (Cole 1986; Spencer and Groudine 1991; Askew et al. 1991; Evan et al. 1992). This is dramatically illustrated by the frequent occurrence of a variety of tumors in many species having alterations of myc genes and the transduction of c-myc sequences by retroviruses (Spencer and Groudine 1991).4+ Eisenman 1990).(ABSTRACT TRUNCATED AT 400 WORDS)
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Affiliation(s)
- S R Hann
- Department of Cell Biology, Vanderbilt Univeristy, School of Medicine, Nashville, Tennessee 37232-2175, USA
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13
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Ozer J, Chalkley R, Sealy L. Characterization of rat pseudogenes for enhancer factor I subunit A: ripping provides clues to the evolution of the EFIA/dbpB/YB-1 multigene family. Gene 1993; 133:187-95. [PMID: 8224907 DOI: 10.1016/0378-1119(93)90637-i] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Genomic Southern blot analysis of rat EFIA (gene encoding enhancer factor I subunit A) reveals a complex band pattern when cDNA subfragment probes are used. Screening a rat genomic library with a rat EFIA cDNA probe yields two different processed EFIA pseudogenes, designated rat psi EFIA#(2/3) and #(4/7), in addition to two other different, but less extensively characterized clones. psi EFIA#(4/7) has no open reading frame (ORF) sequences. psi EFIA#(2/3) contains two ORFs (83 and 178 codons), the products of which (if expressed) might be negative-acting EFIA transcription factors. Located nearly 0.6 kb upstream from psi EFIA#(2/3) is a perfect 69-bp dinucleotide (CT) tandem repeat, a sequence element associated with other isolated pseudogenes. Additionally, the 3' end of this processed gene is interrupted by an unusual retroposon, an inverted dimeric B1-like short interspersed repetitive element (SINE). The isolation of several independent clones of the same EFIA processed pseudogenes indicates that they comprise a significant component of the rat EFIA copy multiplicity. The phenomenon of repeat induced point mutagenesis (ripping) at rat EFIA pseudogene CpG doublets occurs at a frequency at least 6.5 times higher than predicted from random mutagenesis. This is consonant with the proposal that ripping may be the mechanism which inactivates the ectopic recombination potential of the rat EFIA pseudogenes.
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Affiliation(s)
- J Ozer
- Department of Cell Biology, Vanderbilt University School of Medicine, Nashville 37232
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14
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Russell L, Forsdyke DR. The third human homolog of a murine gene encoding an inhibitor of stem cell proliferation is truncated and linked to a CpG island-containing upstream sequence. DNA Cell Biol 1993; 12:157-75. [PMID: 8097094 DOI: 10.1089/dna.1993.12.157] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
The murine gene, MIP1 alpha, encodes a cytokine (macrophage inflammatory protein 1 alpha) that inhibits the proliferation of bone marrow stem cells. Two human homologs have been characterized, G0S19-1 and G0S19-2. Like MIP1 alpha, these genes contain three exons, the first of which encodes a hydrophobic signal sequence. The existence of a third human G0S19 gene, present in one in four individuals, has been predicted from restriction enzyme analyses. This paper reports that a previously identified human genomic clone containing a G0S19 sequence (G0S19-3), corresponds to the third gene. However, the first G0S19 exon is missing. The sequence differs from those of G0S19-1 and G0S19-2 upstream of a point 31 nucleotides from the junction of the first intron with the second exon. This upstream sequence contains a CpG island and is named "CpG island-containing upstream sequence," CUS. Apart from the G0S19-3-associated copy found only in individuals with the third G0S19 gene, all individuals have one DNA species hybridizing strongly to a CUS-specific probe and at least two less strongly hybridizing species. The CUS has potential binding sites for transcription factors AP-1, AP-2, AP-3, AP-4, and Sp1, a Donehower conserved repetitive element, and motifs characteristic of cytokine, oncogene, and retroviral promoters. Thus, the CUS might promote the transcription of sequences with which it became associated. We suggest that the CUS-G0S19-3 sequence was generated by recombination between a G0S19-2 gene and a member of a novel CUS-associated gene family.
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Affiliation(s)
- L Russell
- Department of Biochemistry, Queen's University, Kingston, Ontario, Canada
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15
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Habel DE, Dohrer KL, Conklin KF. Functional and defective components of avian endogenous virus long terminal repeat enhancer sequences. J Virol 1993; 67:1545-54. [PMID: 8382309 PMCID: PMC237525 DOI: 10.1128/jvi.67.3.1545-1554.1993] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
Oncogenic avian retroviruses, such as Rous sarcoma virus (RSV) and the avian leukosis viruses, contain a strong enhancer in the U3 portion of the proviral long terminal repeat (LTR). The LTRs of a second class of avian retroviruses, the endogenous viruses (ev) lack detectable enhancer activity. By creating ev-RSV hybrid LTRs, we previously demonstrated that, despite the lack of independent enhancer activity in the ev U3 region, ev LTRs contain sequences that are able to functionally replace essential enhancer domains from the RSV enhancer. A hypothesis proposed to explain these data was that ev LTRs contain a partial enhancer that includes sequences necessary but not sufficient for enhancer activity and that these sequences were complemented by RSV enhancer domains present in the original hybrid constructs to generate a functional enhancer. Studies described in this report were designed to define sequences from both the ev and RSV LTRs required to generate this composite enhancer. This was approached by generating additional ev-RSV hybrid LTRs that exchanged defined regions between ev and RSV and by directly testing the requirement for specific motifs by site-directed mutagenesis. Results obtained demonstrate that ev enhancer sequences are present in the same relative location as upstream enhancer sequences from RSV, with which they share limited sequence similarity. In addition, a 67-bp region from the internal portion of the RSV LTR that is required to complement ev enhancer sequences was identified. Finally, data showing that CArG motifs are essential for high-level activity, a finding that has not been previously demonstrated for retroviral LTRs, are presented.
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Affiliation(s)
- D E Habel
- Department of Cell and Developmental Biology, University of Minnesota, Minneapolis 55455
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16
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Newby LM, Kulkarni SJ, Jackson FR. Transcriptional organization of a Drosophila glutamic acid decarboxylase gene. J Neurochem 1993; 60:982-9. [PMID: 8436982 DOI: 10.1111/j.1471-4159.1993.tb03245.x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
We previously described the sequence and expression pattern of a Drosophila mRMA (Gad) that encodes the major soluble form of glutamic acid decarboxylase (GAD). We now report the transcriptional organization of the Drosophila Gad gene. Based on a combination of DNA sequence, RNase protection, primer extension, and polymerase chain reaction analyses, we conclude that the transcription unit for a 3.1-kb Gad mRNA is composed of eight exons that span approximately 17-kb genomic interval. By this analysis, the site of Gad transcript initiation overlaps with a recognition sequence that confers binding of the zeste transcription factor to other promoter elements. We emphasize that our analysis of the Gad transcription unit provides no evidence for alternative RNA splicing as a mechanism for the generation of GAD isoforms. Thus, the several GAD-immunoreactive proteins (putative GAD isoforms) that can be detected in Drosophila extracts are probably encoded by distinct genes.
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Affiliation(s)
- L M Newby
- Worcester Foundation for Experimental Biology, Shrewsbury, Massachusetts 01545
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17
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Ozer J, Chalkley R, Sealy L. Isolation of the CCAAT transcription factor subunit EFIA cDNA and a potentially functional EFIA processed pseudogene from Bos taurus: insights into the evolution of the EFIA/dbpB/YB-1 gene family. Gene 1993; 124:223-30. [PMID: 8444345 DOI: 10.1016/0378-1119(93)90397-l] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
The genomic copy multiplicity of the CCAAT transcription complex component enhancer factor I subunit A (EFIA) has been examined. When a mammalian genomic Southern blot was hybridized to a rat EFIA cDNA, a complex pattern consisting of numerous related sequences was found in all the species examined, with Bos taurus being the least complex. An EFIA#1 cDNA from Bos taurus was isolated from a primary lung endothelial cell cDNA library by screening with the 1489-bp rat EFIA cDNA. The deduced bovine EFIA#1 amino acid (aa) sequence is 98% identical to rat EFIA and 100% identical to human EFIA/DbpB/YB-1 family member DNA-binding protein B (DbpB). In addition, a processed EFIA pseudogene from Bos taurus, designated bovine psi EFIA#1, was obtained from a genomic library by screening with a rat EFIA cDNA probe. The bovine psi EFIA#1 gene has an ORF which, if expressed, would encode a 140-aa sequence, with aa 31-140 having 84% identity to bovine EFIA#1. The genomic cloning data indicate that processed pseudogenes are partially responsible for the complexity of the EFIA genomic Southern blots. The phenomenon of 'repeat induced point mutation' (ripping) at bovine psi EFIA#1 gene CpG dinucleotides occurs at a 6.5-fold higher frequency than expected from random mutagenesis. Therefore, ripping is likely to be the mechanism by which the bovine EFIA#1 pseudogene's ectopic recombination potential was inactivated.
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Affiliation(s)
- J Ozer
- Department of Cell Biology, Vanderbilt University Medical Center, Nashville, TN 37232
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18
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Gak E, Yaniv A, Sherman L, Ianconescu M, Tronick SR, Gazit A. Lymphoproliferative disease virus of turkeys: sequence analysis and transcriptional activity of the long terminal repeat. Gene 1991; 99:157-62. [PMID: 2022329 DOI: 10.1016/0378-1119(91)90122-r] [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: 12/29/2022]
Abstract
The lymphoproliferative disease virus (LPDV) is the etiological agent of a lymphoproliferative disease that naturally occurs in turkeys. Recently, we have cloned the LPDV provirus and established it as a replication-competent genome devoid of a viral oncogene [Gak et al., J. Virol. 63 (1989) 2877-2880]. This report presents the nucleotide sequence of its long terminal repeat (LTR) and establishes it as a potent transcriptional element. Several features of the LPDV LTR were similar to those found in the LTRs of the avian sarcoma-leukemia viruses (ASLV) and include the primer-binding site (tRNATrp), the polypurine tract, the organization of the polyadenylation signal, the complexities of the U3, R and U5 regions, as well as a potential secondary structure in U5-R. The LTR sequence diverges significantly from the ASLV LTRs, which share a common structure and have extensive sequence homology mainly in the R and U5 domains. These findings support the conclusion that LPDV represents a distinct class of avian retrovirus, evolutionarily related to the ASLV family.
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Affiliation(s)
- E Gak
- Department of Human Microbiology, Sackler School of Medicine, Tel-Aviv University, Israel
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19
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Ozer J, Faber M, Chalkley R, Sealy L. Isolation and characterization of a cDNA clone for the CCAAT transcription factor EFIA reveals a novel structural motif. J Biol Chem 1990. [DOI: 10.1016/s0021-9258(18)45682-7] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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20
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Faber M, Sealy L. Rous sarcoma virus enhancer factor I is a ubiquitous CCAAT transcription factor highly related to CBF and NF-Y. J Biol Chem 1990. [DOI: 10.1016/s0021-9258(18)45696-7] [Citation(s) in RCA: 29] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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21
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Siddique HR, Sarkar NH. The interaction of a c-Jun/Fos related protein factor with the U3 sequences of the mouse mammary tumor virus LTR. Biochem Biophys Res Commun 1990; 172:348-56. [PMID: 2171522 DOI: 10.1016/s0006-291x(05)80216-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Using polyacrylamide gel mobility shift assay we have detected a nuclear factor (NF-S) in a mouse mammary tumor cell line (GR) that binds to an upstream sequence domain (-766 to -737) near the 5'-end of the mouse mammary tumor virus (MMTV) long terminal repeat (LTR). Antibodies to the products of the Jun and Fos oncogenes interfered with the binding potential of this factor, indicating that the factor shares antigenic determinants with c-Jun/AP-1. In vitro translated c-Jun and c-Fos were also found to bind to the NF-S binding domain consisting of the sequence TGA(A/G)TCA that are known to be recognized by c-Jun/AP-1. Our results raise the possibility that the MMTV-LTR sequence element-766 to -737 by interacting with a Jun/Fos related protein play a role in MMTV transcription and/or the activation of int protooncogenes that are associated with murine mammary tumorigenesis.
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Affiliation(s)
- H R Siddique
- Department of Cell and Molecular Biology, Medical College of Georgia, Augusta 30912-2100
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22
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Sittler AM, Reudelhuber TL. Tissue-specific expression of the rat growth hormone gene is due to the interaction of multiple promoter, not enhancer, elements. DNA Cell Biol 1990; 9:511-8. [PMID: 2222812 DOI: 10.1089/dna.1990.9.511] [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: 12/30/2022] Open
Abstract
Expression of the rat growth hormone (rGH) gene is highly tissue-specific, being limited to a subset of cells in the anterior pituitary. DNA sequences within 237 bp of the transcription start site of the rGH gene play a major role in directing the expression of this gene in the pituitary. Transfection studies in cultured rat pituitary (GC) cells demonstrate that optimal expression of rGH requires the binding of at least two non-tissue-specific factors whose contribution to rGH expression is dependent on the binding of the pituitary-specific factor, Pit-1. Although the segment of DNA containing the elements to which these factors bind can direct pituitary-specific expression of a gene lacking upstream promoter elements, it cannot confer stimulation to either a heterologous or homologous promoter when placed downstream from the coding sequences. These results suggest that expression of the rGH gene exclusively in the pituitary is due to the activity of a tissue-specific promoter element, not an enhancer.
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Affiliation(s)
- A M Sittler
- Department of Medicine and Metabolic Research Unit, University of California, San Francisco 94143
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23
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Nakshatri H, Pater MM, Pater A. Ubiquitous and cell-type-specific protein interactions with human papillomavirus type 16 and type 18 enhancers. Virology 1990; 178:92-103. [PMID: 2167563 DOI: 10.1016/0042-6822(90)90382-2] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
We have studied the protein-DNA interactions of human papillomavirus types 16 and 18 constitutive enhancer elements using DNasel footprinting experiments with nuclear extracts from four cervical carcinoma cell lines (C33A, HeLa, SiHa, and CaSki) and one fibroblast cell line (143B). Among nine footprints for the HPV 16 enhancer region, six footprints contain nuclear factor 1 (NF1) binding GCCAA motif. In vitro competition experiments suggest that the same factors are shared by all six of these motifs. Two other sequence motifs have consensus sequences for transcription factor AP1. Another sequence motif, for which uv crosslinking studies reveal interaction with four protein molecules, is a strong positive modulator of HPV 16 enhancer function in vivo and shares 100% homology to a sequence motif, GTTTTAA, in the tissue-specific enhancer of the c-mos oncogene. Footprints on the HPV 18 enhancer show five protected regions with homologies to NF1, AP1 and EFII transcription factor binding motifs. One sequence motif of the HPV 18 enhancer has three repeats of a TTTTA sequence contained within the c-mos sequence motif and interacts with at least four different individual polypeptides, as judged by uv crosslinking experiments.
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Affiliation(s)
- H Nakshatri
- Division of Basic Medical Sciences, Faculty of Medicine, Memorial University of Newfoundland, St. John's, Canada
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24
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Greuel BT, Sealy L, Majors JE. Transcriptional activity of the Rous sarcoma virus long terminal repeat correlates with binding of a factor to an upstream CCAAT box in vitro. Virology 1990; 177:33-43. [PMID: 2162108 DOI: 10.1016/0042-6822(90)90457-3] [Citation(s) in RCA: 26] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The avian nuclear protein, enhancer factor 1 (EF1), binds specifically to the long terminal repeat (LTR) of Rous sarcoma virus (RSV) in a region that has been implicated in enhancer/promoter function. We have characterized the in vitro binding properties of this factor from chick embryo nuclear extracts by methylation interference/protection foot-printing of the wild-type LTR and also by gel electrophoretic mobility shift assays performed on a series of LTR mutants. We find that the inverted CCAAT pentanucleotide located at position -129 is essential for EF1 binding in vitro. Nucleotides flanking this element exert a smaller effect on binding. Linker-substitution and point mutations which reduce EF1 binding to this site in vitro also reduce promoter activity in transiently transfected cells. EF1 also binds with lower affinity to another inverted CCAAT box at position -65, an element which we show is also essential for transcriptional activity of the RSV LTR. We conclude, therefore, that EF1 is a CCAAT box-binding factor which is involved in the activation of RSV transcription in avian cells. Furthermore, we show that EF1 can recognize the CCAAT boxes of several other promoters in which the functional importance of this pentanucleotide has been established.
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Affiliation(s)
- B T Greuel
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri 63110
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25
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Kenny S, Guntaka RV. Localization by mutational analysis of transcription factor binding sequences in the U3 region of Rous sarcoma virus LTR. Virology 1990; 176:483-93. [PMID: 2161147 DOI: 10.1016/0042-6822(90)90018-m] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The transcription factor binding sequences in the U3 region of Rous Sarcoma virus LTR have been determined by gel retardation assays using mutant synthetic oligonucleotides. The results indicate that the factor, E2BP, specifically binds to sequences TGCAATAC and TGCAACAT, which are localized between nucleotides -222 to -215 and -203 to -196, respectively. This factor is present at elevated levels in avian QT6 cells compared to mouse 3T3 and rat 2 tk- cells. E2BP binds to a sequence that is similar or identical to the sequence recognized by rat liver C/EBP. However, the two proteins are different as judged by three criteria: (i) the E2BP complex migrates slightly faster than the E2-C/EBP complex; (ii) antibodies against C/EBP neither inhibit binding of E2BP nor form a supercomplex which migrates slower than the complex formed with the factor alone; and (iii) E2BP is heat labile whereas C/EBP is heat stable. Another factor, E3BP, which binds to a sequence from -169 to -158, in the U3 region is also detected mainly in QT6 cells but not in mouse or rat cells. These results suggest that different cell-specific factors interact with different cis-acting regulatory sequences in the U3 region of RSV LTR.
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Affiliation(s)
- S Kenny
- Department of Microbiology, School of Medicine, University of Missouri, Columbia 65212
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26
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Kerr LD, Miller DB, Matrisian LM. TGF-beta 1 inhibition of transin/stromelysin gene expression is mediated through a Fos binding sequence. Cell 1990; 61:267-78. [PMID: 2110031 DOI: 10.1016/0092-8674(90)90807-q] [Citation(s) in RCA: 345] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Transforming growth factor beta 1 (TGF-beta 1) inhibits the growth factor and oncogene induction of transin/stromelysin, a secreted matrix-degrading metalloprotease. We demonstrate that a 10 bp element in the transin promoter is required for the TGF-beta 1 inhibitory effects and that this sequence is conserved in the promoter regions of several other TGF-beta 1-inhibited genes. The TGF-beta 1 inhibitory element (TIE) specifically binds a nuclear protein complex from TGF-beta 1-stimulated rat fibroblasts. Interestingly, this complex contained the c-fos proto-oncogene product, Fos, and induction of Fos expression was required for the inhibitory effect of TGF-beta 1 on transin gene expression. These results suggest that TGF-beta 1 inhibition of gene expression is mediated by the binding of a Fos-containing protein complex to the TIE promoter sequences.
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Affiliation(s)
- L D Kerr
- Department of Cell Biology, Vanderbilt University, Nashville, Tennessee 37232
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27
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Boulden A, Sealy L. Identification of a third protein factor which binds to the Rous sarcoma virus LTR enhancer: possible homology with the serum response factor. Virology 1990; 174:204-16. [PMID: 2152992 DOI: 10.1016/0042-6822(90)90069-4] [Citation(s) in RCA: 26] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
We have identified a new protein factor (EFIII) in nuclear extracts of quail fibroblasts and chick embryos which binds specifically in vitro to a 26-bp region of the Rous sarcoma virus (RSV) long terminal repeat (LTR) enhancer. The EFIII binding site in the RSV LTR exhibits a strong sequence homology to the serum response element (SRE). The SRE is a 22-bp cis-acting DNA sequence element, first identified upstream of the human c-fos gene, which can confer serum inducibility to heterologous promotors. The binding site for EFIII in the RSV LTR enhancer is also of interest because this region has been implicated in mediating trans-activation of the RSV LTR enhancer by the protein product of the v-fos gene. We show that avian EFIII binds with equal efficiency to both its binding sites in the RSV LTR and the human c-fos SRE. A dyad symmetry element in the c-fos SRE, previously shown to be critical for binding of the cognate human serum response factor (SRF), is also critical for EFIII binding to the LTR SRE-homologous sequences; similarly, EFIII and the human SRF exhibit identical protein-DNA contacts with their corresponding recognition sequences. We suggest that EFIII may be the avian homolog of the mammalian SRF and, in fact, have evidence to indicate that the RSV LTR is serum responsive.
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Affiliation(s)
- A Boulden
- Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, Tennessee 37232
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28
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Affiliation(s)
- J Majors
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO 63110
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29
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Binninger D, Ferdinand FJ, Rübsamen-Waigmann H. Inhibition of SV40 DNA replication by Rous sarcoma virus LTR enhancer. Arch Virol 1989; 107:291-9. [PMID: 2554858 DOI: 10.1007/bf01317924] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Simian virus 40 (SV40) late region recombinant constructs containing the Rous sarcoma virus (RSV) src gene along with RSV enhancer stimulated expression but completely abolished SV40 DNA replication. Constructs, in which the heterologous enhancer sequences were omitted, did replicate normally in African green monkey kidney cells and, in the presence of helper virus, gave rise to infectious progeny. Inhibition of SV40 DNA replication follows a cis-acting mechanism and is most likely due to a conformational change of the SV40 chromatin structure.
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Affiliation(s)
- D Binninger
- Chemotherapeutisches Forschungsinstitut Georg-Speyer-Haus, Frankfurt/Main, Federal Republic of Germany
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30
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Ballard DW, Philbrick WM, Bothwell AL. Identification of a novel 9-kDa polypeptide from nuclear extracts. DNA binding properties, primary structure, and in vitro expression. J Biol Chem 1988. [DOI: 10.1016/s0021-9258(18)68498-4] [Citation(s) in RCA: 16] [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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31
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Gowda S, Rao AS, Kim YW, Guntaka RV. Identification of sequences in the long terminal repeat of avian sarcoma virus required for efficient transcription. Virology 1988; 162:243-7. [PMID: 2827383 DOI: 10.1016/0042-6822(88)90415-1] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Two different vectors, LTR-NEO-LTR and LTR-CAT-LTR, were constructed and deletions were introduced in the upstream LTR at -299 and at -140. These deletion mutants were introduced into QT6 cells under transient expression conditions, and the levels of transcription were monitored by dot blot hybridization or by CAT assays. The results indicate that the nucleotides between -208 and -201 and between -141 and -119 in the U3 region of RSV LTR are required for efficient transcription.
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Affiliation(s)
- S Gowda
- Department of Microbiology, School of Medicine, University of Missouri-Columbia 65212
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32
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Affiliation(s)
- C M Stoltzfus
- Department of Microbiology, University of Iowa, Iowa City 52242
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