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Shao T, Pan YH, Xiong XD. Circular RNA: an important player with multiple facets to regulate its parental gene expression. MOLECULAR THERAPY-NUCLEIC ACIDS 2020; 23:369-376. [PMID: 33425494 PMCID: PMC7779830 DOI: 10.1016/j.omtn.2020.11.008] [Citation(s) in RCA: 73] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Circular RNAs (circRNAs), a novel type of endogenous RNAs with covalently closed-loop structures, have become a new research hotspot in the RNA world. Their diversity, stability, evolutionary conservation, and cell type- or tissue-specific expression patterns endow circRNAs with various important biological functions. As a consequence, circRNAs are emerging as important regulators of physiological development and disease pathogenesis. Growing evidence has shown that circRNAs can regulate parental gene expression through diverse mechanisms, such as transcription and splicing regulation, microRNA (miRNA) sponges, mRNA traps, translational modulation, and post-translational modification. The study of circRNAs and how circRNAs regulate the expression of parental genes will facilitate a deeper understanding of their biological functions and provide new perspectives on their clinical application. Herein, we review the biogenesis of circRNAs, with a particular focus on the molecular mechanisms of circRNAs regulating their parental gene expression and the biological significance of such regulation.
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Affiliation(s)
- Tong Shao
- Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, Institute of Aging Research, Guangdong Medical University, Dongguan 523808, P.R. China.,Institute of Biochemistry & Molecular Biology, Guangdong Medical University, Zhanjiang 524023, P.R. China
| | - Yan-Hong Pan
- Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, Institute of Aging Research, Guangdong Medical University, Dongguan 523808, P.R. China.,Institute of Biochemistry & Molecular Biology, Guangdong Medical University, Zhanjiang 524023, P.R. China
| | - Xing-Dong Xiong
- Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, Institute of Aging Research, Guangdong Medical University, Dongguan 523808, P.R. China.,Institute of Biochemistry & Molecular Biology, Guangdong Medical University, Zhanjiang 524023, P.R. China
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Guiro J, Murphy S. Regulation of expression of human RNA polymerase II-transcribed snRNA genes. Open Biol 2018; 7:rsob.170073. [PMID: 28615474 PMCID: PMC5493778 DOI: 10.1098/rsob.170073] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2017] [Accepted: 05/11/2017] [Indexed: 12/31/2022] Open
Abstract
In addition to protein-coding genes, RNA polymerase II (pol II) transcribes numerous genes for non-coding RNAs, including the small-nuclear (sn)RNA genes. snRNAs are an important class of non-coding RNAs, several of which are involved in pre-mRNA splicing. The molecular mechanisms underlying expression of human pol II-transcribed snRNA genes are less well characterized than for protein-coding genes and there are important differences in expression of these two gene types. Here, we review the DNA features and proteins required for efficient transcription of snRNA genes and co-transcriptional 3′ end formation of the transcripts.
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Affiliation(s)
- Joana Guiro
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Shona Murphy
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
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Amin KS, Jagadeesh S, Baishya G, Rao PG, Barua NC, Bhattacharya S, Banerjee PP. A naturally derived small molecule disrupts ligand-dependent and ligand-independent androgen receptor signaling in human prostate cancer cells. Mol Cancer Ther 2013; 13:341-52. [PMID: 24258347 DOI: 10.1158/1535-7163.mct-13-0478] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Continued reliance on androgen receptor (AR) signaling is a hallmark of prostate cancer, including the development of castration-resistant prostate cancer (CRPC), making it an attractive therapeutic target for prostate cancer treatment. Mahanine is a novel carbazole alkaloid derived from the leaves of Murraya koenigii, commonly known as the curry leaf plant, which grows widely across East-Asia. We show here that mahanine possesses the ability to inhibit ligand-dependent and -independent AR transactivation, leading to a prominent decline in AR target gene expression. Mahanine treatment causes a time- and dose-dependent decline in AR protein levels, including truncated AR splice variants, in a panel of androgen-responsive and -independent prostate cancer cells. The decrease in AR levels induced by mahanine occurs posttranslationally by proteasomal degradation, without any change in the AR gene expression. Mahanine treatment induces an outward movement of the AR from the nucleus to the cytoplasm, leading to an initial increase in cytoplasmic AR levels, followed by a gradual decline in the AR levels in both cellular compartments. Ligand-induced AR phosphorylation at Ser-81, a phospho-site associated with prostate cancer cell growth and AR transactivity, is greatly diminished in the presence of mahanine. The decline in AR phosphorylation at Ser-81 by mahanine occurs via the inactivation of mitotic kinase CDK1. Collectively, our data demonstrate that mahanine strongly disrupts AR signaling and inhibits the growth of androgen-dependent and -independent prostate cancer cells, thereby implicating a therapeutic role of mahanine in prostate cancer treatment.
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Affiliation(s)
- Karishma S Amin
- Corresponding Author: Partha P. Banerjee, Department of Biochemistry and Molecular & Cellular Biology, Georgetown University Medical Center, 3900 Reservoir Road, NW, Washington, DC 20057.
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Zaborowska J, Taylor A, Roeder RG, Murphy S. A novel TBP-TAF complex on RNA polymerase II-transcribed snRNA genes. Transcription 2012; 3:92-104. [PMID: 22441827 PMCID: PMC3337830 DOI: 10.4161/trns.19783] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Initiation of transcription of most human genes transcribed by RNA polymerase II (RNAP II) requires the formation of a preinitiation complex comprising TFIIA, B, D, E, F, H and RNAP II. The general transcription factor TFIID is composed of the TATA-binding protein and up to 13 TBP-associated factors. During transcription of snRNA genes, RNAP II does not appear to make the transition to long-range productive elongation, as happens during transcription of protein-coding genes. In addition, recognition of the snRNA gene-type specific 3′ box RNA processing element requires initiation from an snRNA gene promoter. These characteristics may, at least in part, be driven by factors recruited to the promoter. For example, differences in the complement of TAFs might result in differential recruitment of elongation and RNA processing factors. As precedent, it already has been shown that the promoters of some protein-coding genes do not recruit all the TAFs found in TFIID. Although TAF5 has been shown to be associated with RNAP II-transcribed snRNA genes, the full complement of TAFs associated with these genes has remained unclear. Here we show, using a ChIP and siRNA-mediated approach, that the TBP/TAF complex on snRNA genes differs from that found on protein-coding genes. Interestingly, the largest TAF, TAF1, and the core TAFs, TAF10 and TAF4, are not detected on snRNA genes. We propose that this snRNA gene-specific TAF subset plays a key role in gene type-specific control of expression.
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Konduri SD, Medisetty R, Liu W, Kaipparettu BA, Srivastava P, Brauch H, Fritz P, Swetzig WM, Gardner AE, Khan SA, Das GM. Mechanisms of estrogen receptor antagonism toward p53 and its implications in breast cancer therapeutic response and stem cell regulation. Proc Natl Acad Sci U S A 2010; 107:15081-6. [PMID: 20696891 PMCID: PMC2930589 DOI: 10.1073/pnas.1009575107] [Citation(s) in RCA: 91] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
Estrogen receptor alpha (ERalpha) plays an important role in the onset and progression of breast cancer, whereas p53 functions as a major tumor suppressor. We previously reported that ERalpha binds to p53, resulting in inhibition of transcriptional regulation by p53. Here, we report on the molecular mechanisms by which ERalpha suppresses p53's transactivation function. Sequential ChIP assays demonstrated that ERalpha represses p53-mediated transcriptional activation in human breast cancer cells by recruiting nuclear receptor corepressors (NCoR and SMRT) and histone deacetylase 1 (HDAC1). RNAi-mediated down-regulation of NCoR resulted in increased endogenous expression of the cyclin-dependent kinase (CDK)-inhibitor p21(Waf1/Cip1) (CDKN1A) gene, a prototypic transcriptional target of p53. While 17beta-estradiol (E2) enhanced ERalpha binding to p53 and inhibited p21 transcription, antiestrogens decreased ERalpha recruitment and induced transcription. The effects of estrogen and antiestrogens on p21 transcription were diametrically opposite to their known effects on the conventional ERE-containing ERalpha target gene, pS2/TFF1. These results suggest that ERalpha uses dual strategies to promote abnormal cellular proliferation: enhancing the transcription of ERE-containing proproliferative genes and repressing the transcription of p53-responsive antiproliferative genes. Importantly, ERalpha binds to p53 and inhibits transcriptional activation by p53 in stem/progenitor cell-containing murine mammospheres, suggesting a potential role for the ER-p53 interaction in mammary tissue homeostasis and cancer formation. Furthermore, retrospective studies analyzing response to tamoxifen therapy in a subset of patients with ER-positive breast cancer expressing either wild-type or mutant p53 suggest that the presence of wild-type p53 is an important determinant of positive therapeutic response.
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Affiliation(s)
- Santhi D. Konduri
- aDepartment of Pharmacology and Therapeutics, Center for Genetics and Pharmacology, Roswell Park Cancer Institute, Buffalo, NY 14263
| | - Rajesh Medisetty
- aDepartment of Pharmacology and Therapeutics, Center for Genetics and Pharmacology, Roswell Park Cancer Institute, Buffalo, NY 14263
| | - Wensheng Liu
- aDepartment of Pharmacology and Therapeutics, Center for Genetics and Pharmacology, Roswell Park Cancer Institute, Buffalo, NY 14263
| | - Benny Abraham Kaipparettu
- bDr. Margarete Fischer-Bosch-Institute of Clinical Pharmacology, D 70376 Stuttgart, Germany
- cUniversity Tuebingen, D 72074 Tuebingen, Germany
| | - Pratima Srivastava
- aDepartment of Pharmacology and Therapeutics, Center for Genetics and Pharmacology, Roswell Park Cancer Institute, Buffalo, NY 14263
| | - Hiltrud Brauch
- bDr. Margarete Fischer-Bosch-Institute of Clinical Pharmacology, D 70376 Stuttgart, Germany
- cUniversity Tuebingen, D 72074 Tuebingen, Germany
| | - Peter Fritz
- bDr. Margarete Fischer-Bosch-Institute of Clinical Pharmacology, D 70376 Stuttgart, Germany
- cUniversity Tuebingen, D 72074 Tuebingen, Germany
| | - Wendy M. Swetzig
- aDepartment of Pharmacology and Therapeutics, Center for Genetics and Pharmacology, Roswell Park Cancer Institute, Buffalo, NY 14263
| | - Amanda E. Gardner
- dDepartment of Cancer and Cell Biology, Vontz Center for Molecular Studies, University of Cincinnati College of Medicine, Cincinnati, OH 45267
| | - Sohaib A. Khan
- dDepartment of Cancer and Cell Biology, Vontz Center for Molecular Studies, University of Cincinnati College of Medicine, Cincinnati, OH 45267
| | - Gokul M. Das
- aDepartment of Pharmacology and Therapeutics, Center for Genetics and Pharmacology, Roswell Park Cancer Institute, Buffalo, NY 14263
- 6To whom correspondence should be addressed. E-mail:
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Desmazières A, Charnay P, Gilardi-Hebenstreit P. Krox20 controls the transcription of its various targets in the developing hindbrain according to multiple modes. J Biol Chem 2009; 284:10831-40. [PMID: 19218566 DOI: 10.1074/jbc.m808683200] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
The zinc finger transcription factor Krox20 plays an essential role in the vertebrate hindbrain segmentation process. It positively or negatively controls a large variety of other regulatory genes, coordinating delimitation of segmental territories, specification of their identity, and maintenance of their integrity. We have investigated the molecular mechanisms of Krox20 transcriptional control by performing a detailed structure-function analysis of the protein in the developing chick hindbrain. This revealed an unsuspected diversity in the modes of action of a transcription factor in a single tissue, since regulation of each of the five tested target genes requires different parts of the protein and/or presumably different co-factors. The multiplicity of Krox20 functions might rely on this diversity. Investigation of known Krox20 co-factors was initiated in relation to this analysis. Nab was shown to act as a negative feedback modulator of the different Krox20 activating functions in the hindbrain. HCF-1 was found to bind to a Krox20 N-terminal region, which was shown to rely on multiple elements, including acidic domains, to convey Nab activation and Krox20 autoregulation.
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Langlois C, Mas C, Di Lello P, Jenkins LMM, Legault P, Omichinski JG. NMR Structure of the Complex between the Tfb1 Subunit of TFIIH and the Activation Domain of VP16: Structural Similarities between VP16 and p53. J Am Chem Soc 2008; 130:10596-604. [DOI: 10.1021/ja800975h] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Chantal Langlois
- Département de Biochimie, Université de Montréal, C.P. 6128 Succursale Centre-Ville, Montréal, QC H3C 3J7 Canada, and Laboratory of Cell Biology, NCI, National Institutes of Health, 37 Convent Drive, Bethesda, Maryland 20892-4256
| | - Caroline Mas
- Département de Biochimie, Université de Montréal, C.P. 6128 Succursale Centre-Ville, Montréal, QC H3C 3J7 Canada, and Laboratory of Cell Biology, NCI, National Institutes of Health, 37 Convent Drive, Bethesda, Maryland 20892-4256
| | - Paola Di Lello
- Département de Biochimie, Université de Montréal, C.P. 6128 Succursale Centre-Ville, Montréal, QC H3C 3J7 Canada, and Laboratory of Cell Biology, NCI, National Institutes of Health, 37 Convent Drive, Bethesda, Maryland 20892-4256
| | - Lisa M. Miller Jenkins
- Département de Biochimie, Université de Montréal, C.P. 6128 Succursale Centre-Ville, Montréal, QC H3C 3J7 Canada, and Laboratory of Cell Biology, NCI, National Institutes of Health, 37 Convent Drive, Bethesda, Maryland 20892-4256
| | - Pascale Legault
- Département de Biochimie, Université de Montréal, C.P. 6128 Succursale Centre-Ville, Montréal, QC H3C 3J7 Canada, and Laboratory of Cell Biology, NCI, National Institutes of Health, 37 Convent Drive, Bethesda, Maryland 20892-4256
| | - James G. Omichinski
- Département de Biochimie, Université de Montréal, C.P. 6128 Succursale Centre-Ville, Montréal, QC H3C 3J7 Canada, and Laboratory of Cell Biology, NCI, National Institutes of Health, 37 Convent Drive, Bethesda, Maryland 20892-4256
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Jawdekar GW, Henry RW. Transcriptional regulation of human small nuclear RNA genes. BIOCHIMICA ET BIOPHYSICA ACTA 2008; 1779:295-305. [PMID: 18442490 PMCID: PMC2684849 DOI: 10.1016/j.bbagrm.2008.04.001] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2007] [Revised: 04/01/2008] [Accepted: 04/02/2008] [Indexed: 01/06/2023]
Abstract
The products of human snRNA genes have been frequently described as performing housekeeping functions and their synthesis refractory to regulation. However, recent studies have emphasized that snRNA and other related non-coding RNA molecules control multiple facets of the central dogma, and their regulated expression is critical to cellular homeostasis during normal growth and in response to stress. Human snRNA genes contain compact and yet powerful promoters that are recognized by increasingly well-characterized transcription factors, thus providing a premier model system to study gene regulation. This review summarizes many recent advances deciphering the mechanism by which the transcription of human snRNA and related genes are regulated.
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Affiliation(s)
- Gauri W. Jawdekar
- Department of Microbiology, Immunology, and Molecular Genetics, University of California at Los Angeles, Los Angeles, CA 90095
| | - R. William Henry
- Department of Biochemistry & Molecular Biology, Michigan State University, East Lansing, MI 48824
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Lentiviral vectors encoding tetracycline-dependent repressors and transactivators for reversible knockdown of gene expression: a comparative study. BMC Biotechnol 2007; 7:41. [PMID: 17634114 PMCID: PMC1959519 DOI: 10.1186/1472-6750-7-41] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2006] [Accepted: 07/16/2007] [Indexed: 12/02/2022] Open
Abstract
Background RNA interference (RNAi)-mediated by the expression of short hairpin RNAs (shRNAs) has emerged as a powerful experimental tool for reverse genetic studies in mammalian cells. A number of recent reports have described approaches allowing regulated production of shRNAs based on modified RNA polymerase II (Pol II) or RNA polymerase III (Pol III) promoters, controlled by drug-responsive transactivators or repressors such as tetracycline (Tet)-dependent transactivators and repressors. However, the usefulness of these approaches is often times limited, caused by inefficient delivery and/or expression of shRNA-encoding sequences in target cells and/or poor design of shRNAs sequences. With a view toward optimizing Tet-regulated shRNA expression in mammalian cells, we compared the capacity of a variety of hybrid Pol III promoters to express short shRNAs in target cells following lentivirus-mediated delivery of shRNA-encoding cassettes. Results RNAi-mediated knockdown of gene expression in target cells, controlled by a modified Tet-repressor (TetR) in the presence of doxycycline (Dox) was robust. Expression of shRNAs from engineered human U6 (hU6) promoters containing a single tetracycline operator (TO) sequence between the proximal sequence element (PSE) and the TATA box, or an improved second-generation Tet-responsive promoter element (TRE) placed upstream of the promoter was tight and reversible as judged using quantitative protein measurements. We also established and tested a novel hU6 promoter system in which the distal sequence element (DSE) of the hU6 promoter was replaced with a second-generation TRE. In this system, positive regulation of shRNA production is mediated by novel Tet-dependent transactivators bearing transactivation domains derived from the human Sp1 transcription factor. Conclusion Our modified lentiviral vector system resulted in tight and reversible knockdown of target gene expression in unsorted cell populations. Tightly regulated target gene knockdown was observed with vectors containing either a single TO sequence or a second-generation TRE using carefully controlled transduction conditions. We expect these vectors to ultimately find applications for tight and reversible RNAi in mammalian cells in vivo.
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Zhu W, Wada T, Okabe S, Taneda T, Yamaguchi Y, Handa H. DSIF contributes to transcriptional activation by DNA-binding activators by preventing pausing during transcription elongation. Nucleic Acids Res 2007; 35:4064-75. [PMID: 17567605 PMCID: PMC1919491 DOI: 10.1093/nar/gkm430] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
The transcription elongation factor 5,6-dichloro-1-β-d-ribofuranosylbenzimidazole (DRB) sensitivity-inducing factor (DSIF) regulates RNA polymerase II (RNAPII) processivity by promoting, in concert with negative elongation factor (NELF), promoter-proximal pausing of RNAPII. DSIF is also reportedly involved in transcriptional activation. However, the role of DSIF in transcriptional activation by DNA-binding activators is unclear. Here we show that DSIF acts cooperatively with a DNA-binding activator, Gal4-VP16, to promote transcriptional activation. In the absence of DSIF, Gal4-VP16-activated transcription resulted in frequent pausing of RNAPII during elongation in vitro. The presence of DSIF reduced pausing, thereby supporting Gal4-VP16-mediated activation. We found that DSIF exerts its positive effects within a short time-frame from initiation to elongation, and that NELF does not affect the positive regulatory function of DSIF. Knockdown of the gene encoding the large subunit of DSIF, human Spt5 (hSpt5), in HeLa cells reduced Gal4-VP16-mediated activation of a reporter gene, but had no effect on expression in the absence of activator. Together, these results provide evidence that higher-level transcription has a stronger requirement for DSIF, and that DSIF contributes to efficient transcriptional activation by preventing RNAPII pausing during transcription elongation.
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Affiliation(s)
- Wenyan Zhu
- Graduate School of Bioscience and Biotechnology and Integrated Research Institute, Tokyo Institute of Technology, 4259 Nagatsuta, Midori-ku, Yokohama 226-8501, Japan
| | - Tadashi Wada
- Graduate School of Bioscience and Biotechnology and Integrated Research Institute, Tokyo Institute of Technology, 4259 Nagatsuta, Midori-ku, Yokohama 226-8501, Japan
- *To whom correspondence should be addressed. +81-45-924-5798+81-45-924-5834,
| | - Sachiko Okabe
- Graduate School of Bioscience and Biotechnology and Integrated Research Institute, Tokyo Institute of Technology, 4259 Nagatsuta, Midori-ku, Yokohama 226-8501, Japan
| | - Takuya Taneda
- Graduate School of Bioscience and Biotechnology and Integrated Research Institute, Tokyo Institute of Technology, 4259 Nagatsuta, Midori-ku, Yokohama 226-8501, Japan
| | - Yuki Yamaguchi
- Graduate School of Bioscience and Biotechnology and Integrated Research Institute, Tokyo Institute of Technology, 4259 Nagatsuta, Midori-ku, Yokohama 226-8501, Japan
| | - Hiroshi Handa
- Graduate School of Bioscience and Biotechnology and Integrated Research Institute, Tokyo Institute of Technology, 4259 Nagatsuta, Midori-ku, Yokohama 226-8501, Japan
- *To whom correspondence should be addressed. +81-45-924-5798+81-45-924-5834,
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Amir-Zilberstein L, Ainbinder E, Toube L, Yamaguchi Y, Handa H, Dikstein R. Differential regulation of NF-kappaB by elongation factors is determined by core promoter type. Mol Cell Biol 2007; 27:5246-59. [PMID: 17502349 PMCID: PMC1951948 DOI: 10.1128/mcb.00586-07] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
NF-kappaB transcription factors activate genes important for immune response, inflammation, and cell survival. P-TEFb and DSIF, which are positive and negative transcription elongation factors, respectively, both regulate NF-kappaB-induced transcription, but the mechanism underlying their recruitment to NF-kappaB target genes is unknown. We show here that upon induction of NF-kappaB, a subset of target genes is regulated differentially by either P-TEFb or DSIF. The regulation of these genes and their occupancy by these elongation factors are dependent on the NF-kappaB enhancer and the core promoter type. Converting a TATA-less promoter to a TATA promoter switches the regulation of NF-kappaB from DSIF to P-TEFb. Accumulation or displacement of DSIF and P-TEFb is dictated by the formation of distinct initiation complexes (TFIID dependent or independent) on the two types of core promoter. The underlying mechanism for the dissociation of DSIF from TATA promoters upon NF-kappaB activation involves the phosphorylation of RNA polymerase II by P-TEFb. The results highlight a regulatory link between the initiation and the elongation phases of the transcription reaction and broaden our comprehension of the NF-kappaB pathway.
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Affiliation(s)
- Liat Amir-Zilberstein
- Department of Biological Chemistry, The Weizmann Institute of Science, Rehovot 76100, Israel
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12
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Fei Z, Chen Z, Wang Z, Fei J. Conditional RNA interference achieved by Oct-1 POU/rtTA fusion protein activator and a modified TRE-mouse U6 promoter. Biochem Biophys Res Commun 2007; 354:906-12. [PMID: 17276396 DOI: 10.1016/j.bbrc.2007.01.081] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2006] [Accepted: 01/14/2007] [Indexed: 11/23/2022]
Abstract
RNA interference (RNAi) is a powerful technique and is widely used to down-regulate expression of specific genes in cultured cells and in vivo. In this paper, we report our development of a new tetracycline-inducible RNAi expression using a modified TRE-mouse U6 promoter in which the distal sequence element (DSE) was replaced by the tetracycline-responsive element (TRE). The modified TRE-mouse U6 promoter can be activated by a Tet-on version tetracycline-regulated artificial activator rTetOct which was constructed by fusing the rtTA DNA binding domain with the Oct-1 POU activation domain. This rTetOct/TRE-U6 system was successfully applied to conditionally and reversibly down-regulate the expression of endogenous p53 gene in MCF7 cells, and the expression of beta-defensin gene (mBin1b) either transiently expressed in COS7 cells or stably expressed in CHO cells.
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Affiliation(s)
- Zhaoliang Fei
- Laboratory of Molecular Cell Biology, Institute of Biochemistry and Cell Biology, Model Organism Research Center, SIBS, CAS, Shanghai, China
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Amar L, Desclaux M, Faucon-Biguet N, Mallet J, Vogel R. Control of small inhibitory RNA levels and RNA interference by doxycycline induced activation of a minimal RNA polymerase III promoter. Nucleic Acids Res 2006; 34:e37. [PMID: 16522642 PMCID: PMC1390691 DOI: 10.1093/nar/gkl034] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
RNA interference (RNAi) mediated by expression of short hairpin RNAs (shRNAs) is a powerful tool for efficiently suppressing target genes. The approach allows studies of the function of individual genes and may also be applied to human therapy. However, in many instances regulation of RNAi by administration of a small inducer molecule will be required. To date, the development of appropriate regulatory systems has been hampered by the few possibilities for modification within RNA polymerase III promoters capable of driving efficient expression of shRNAs. We have developed an inducible minimal RNA polymerase III promoter that is activated by a novel recombinant transactivator in the presence of doxycycline (Dox). The recombinant transactivator and the engineered promoter together form a system permitting regulation of RNAi by Dox-induced expression of shRNAs. Regulated RNAi was mediated by one single lentiviral vector, blocked the expression of green fluorescent protein (GFP) in a GFP-expressing HEK 293T derived cell line and suppressed endogenous p53 in wild-type HEK 293T, MCF-7 and A549 cells. RNA interference was induced in a dose- and time-dependent manner by administration of Dox, silenced the expression of both target genes by 90% and was in particular reversible after withdrawal of Dox.
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Affiliation(s)
| | | | | | - Jacques Mallet
- To whom correspondence should be addressed. Tel: +33 1 42 17 75 32; Fax: +33 1 42 17 75 33;
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Liu W, Konduri SD, Bansal S, Nayak BK, Rajasekaran SA, Karuppayil SM, Rajasekaran AK, Das GM. Estrogen receptor-alpha binds p53 tumor suppressor protein directly and represses its function. J Biol Chem 2006; 281:9837-40. [PMID: 16469747 DOI: 10.1074/jbc.c600001200] [Citation(s) in RCA: 120] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Estrogen receptor-alpha (ERalpha) promotes proliferation of breast cancer cells, whereas tumor suppressor protein p53 impedes proliferation of cells with genomic damage. Whether there is a direct link between these two antagonistic pathways has remained unclear. Here we report that ERalpha binds directly to p53 and represses its function. The activation function-2 (AF-2) domain of ERalpha and the C-terminal regulatory domain of p53 are necessary for the interaction. Knocking down p53 and ERalpha by small interfering RNA elicits opposite effects on p53-target gene expression and cell cycle progression. Remarkably, ionizing radiation that causes genomic damage disrupts the interaction between ERalpha and p53. Ionizing radiation together with ERalpha knock down results in additive effect on transcription of endogenous p53-target gene p21 (CDKN1) in human breast cancer cells. Our findings reveal a novel mechanism for regulating p53 and suggest that suppressing p53 function is an important component in the pro-proliferative role of ERalpha.
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Affiliation(s)
- Wensheng Liu
- Department of Pharmacology and Therapeutics, Roswell Park Cancer Institute, Elm & Carlton Sts., Buffalo, NY 14263, USA
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Karzenowski D, Potter DW, Padidam M. Inducible control of transgene expression with ecdysone receptor: gene switches with high sensitivity, robust expression, and reduced size. Biotechniques 2005; 39:191-2, 194, 196 passim. [PMID: 16116792 DOI: 10.2144/05392st01] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
The ecdysone receptor (EcR)-based gene regulation system is a tool for controlling gene expression. To improve the sensitivity of this system, we evaluated many two-hybrid format synthetic gene constructs in which the GAL4 DNA binding domain was fused to the ligand binding domain of the Choristoneura fumiferana EcR mutant V390I/Y410E (GEvy), and various activation domains--VP16, p53, p65, or E2F-i--were fused to the EF domains of chimeric human RXR. These gene switches were assayed in NIH3T3 cells, HEK293 cells, and in mouse quadriceps in the presence of the nonsteroidal inducer RG-115819 or GS-E. All of the two-hybrid format constructs had no or very low background in the "off" condition and high luciferase reporter gene expression levels in "on" conditions. Extremely high sensitivity was achieved, with EC50 values in the subnanomolar range and with maximal induction at 10 nM RG-115819. Co-expression of both receptor genes with encephalomyocarditis virus (EMCV) or eIF4G internal ribosome entry site (IRES) sequences gave robust induction levels. To reduce the size of the switch construct, we tested single receptor formats, in which any of 14 different activation domains were fused to GEvy. We identified several switches with acceptable levels of basal and maximal induction levels. The gene switches described here provide receptor configuration options suitable for gene function studies, therapeutic protein production in cell culture, transgenic mouse models, and gene/cell therapy.
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17
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Lynch M, Chen L, Ravitz MJ, Mehtani S, Korenblat K, Pazin MJ, Schmidt EV. hnRNP K binds a core polypyrimidine element in the eukaryotic translation initiation factor 4E (eIF4E) promoter, and its regulation of eIF4E contributes to neoplastic transformation. Mol Cell Biol 2005; 25:6436-53. [PMID: 16024782 PMCID: PMC1190351 DOI: 10.1128/mcb.25.15.6436-6453.2005] [Citation(s) in RCA: 96] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2004] [Revised: 12/23/2004] [Accepted: 05/02/2005] [Indexed: 11/20/2022] Open
Abstract
Translation initiation factor eukaryotic translation initiation factor 4E (eIF4E) plays a key role in regulation of cellular proliferation. Its effects on the m7GpppN mRNA cap are critical because overexpression of eIF4E transforms cells, and eIF4E function is rate-limiting for G1 passage. Although we identified eIF4E as a c-Myc target, little else is known about its transcriptional regulation. Previously, we described an element at position -25 (TTACCCCCCCTT) that was critical for eIF4E promoter function. Here we report that this sequence (named 4EBE, for eIF4E basal element) functions as a basal promoter element that binds hnRNP K. The 4EBE is sufficient to replace TATA sequences in a heterologous reporter construct. Interactions between 4EBE and upstream activator sites are position, distance, and sequence dependent. Using DNA affinity chromatography, we identified hnRNP K as a 4EBE-binding protein. Chromatin immunoprecipitation, siRNA interference, and hnRNP K overexpression demonstrate that hnRNP K can regulate eIF4E mRNA. Moreover, hnRNP K increased translation initiation, increased cell division, and promoted neoplastic transformation in an eIF4E-dependent manner. hnRNP K binds the TATA-binding protein, explaining how the 4EBE might replace TATA in the eIF4E promoter. hnRNP K is an unusually diverse regulator of multiple steps in growth regulation because it also directly regulates c-myc transcription, mRNA export, splicing, and translation initiation.
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Affiliation(s)
- Mary Lynch
- Cancer Research Center at Massachusetts General Hospital and Harvard Medical School, 55 Fruit St., Boston, MA 02114, USA
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18
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Dorval KM, Bobechko BP, Ahmad KF, Bremner R. Transcriptional activity of the paired-like homeodomain proteins CHX10 and VSX1. J Biol Chem 2005; 280:10100-8. [PMID: 15647262 DOI: 10.1074/jbc.m412676200] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
CHX10 and VSX1 are homeodomain (HD) proteins essential for normal retinal development. CHX10 is required first for retinal progenitor cell proliferation and later for bipolar cell differentiation, whereas VSX1 is important in the terminal differentiation of a subset of bipolar cells. Elucidating the transcriptional activity of CHX10 and VSX1 is required to understand how these factors control retinal development. We show that CHX10 and Vsx1 can function as transcriptional repressors. When tethered to a promoter by a heterologous LexA DNA-binding domain or its HD, CHX10 repressed multiple classes of activators in different immortalized cell lines. CHX10 blocked TATA-containing and TATA-less promoters, repressed at a distance, and inhibited a complex enhancer positioned upstream or downstream of the reporter gene, whereas retinoblastoma protein (RB) inhibited the downstream enhancer only. Interestingly, CHX10 mildly potentiated a subset of activators in chick neuronal cultures. Thus, CHX10 is both a versatile repressor and a context-specific weak activator. The CHX10 HD and CVC domains were sufficient for DNA binding and repression. VSX1 contains closely related homeo and CVC domains and, like CHX10, also repressed transcription. A VSX1 HD mutation, R166W, that impairs DNA binding and causes keratoconus in humans, hindered repressor function. Therefore, CHX10 and VSX1 may control retinal bipolar cell specification or differentiation by repressing genes required for the development of other cell types.
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Affiliation(s)
- Kimberley M Dorval
- Toronto Western Research Institute, University Health Network Program, University of Toronto, Toronto, Ontario M5T 2S8, Canada
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19
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Narayan S, Jaiswal AS, Kang D, Srivastava P, Das GM, Gairola CG. Cigarette smoke condensate-induced transformation of normal human breast epithelial cells in vitro. Oncogene 2004; 23:5880-9. [PMID: 15208684 DOI: 10.1038/sj.onc.1207792] [Citation(s) in RCA: 56] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2004] [Revised: 04/06/2004] [Accepted: 04/06/2004] [Indexed: 12/21/2022]
Abstract
In the present study, we showed that a single-dose treatment of normal breast epithelial cell line, MCF10A, for 72 h with cigarette smoke condensate (CSC) resulted in a transformed phenotype. The anchorage-dependent growth of these cells was decreased due to increased cell cycle arrest in S-G2/M phase; however, the surviving cells developed resistance due to an increased Bcl-xL to Bax ratio. Levels of PCNA and gadd45 proteins--involved in DNA repair in response to genomic damage--were increased, suggesting that the cells were responding to CSC-induced genomic damage. The transformation of MCF10A cells was determined by their colony-forming efficiency in soft-agar in an anchorage-independent manner. CSC-treated MCF10A cells efficiently formed colonies in soft-agar. We then re-established cell lines from the soft-agar colonies and further examined the persistence of their transforming characteristics. The re-established cell lines, when plated after 17 passages without CSC treatment, still formed colonies in the soft-agar. An increased staining of neuropilin-1 (NRP-1) further showed a transformation characteristic of MCF10A cells treated with CSC. In summary, our results suggest that CSC is capable of transforming the MCF10A cells in vitro, supporting the role of cigarette smoking and increased risk for breast cancer.
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Affiliation(s)
- Satya Narayan
- Department of Anatomy and Cell Biology, UF Shands Cancer Center, Academic Research Building, Room R4-216, PO Box 100232, University of Florida, Gainesville, FL 32610, USA.
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20
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Gupta S, Schoer RA, Egan JE, Hannon GJ, Mittal V. Inducible, reversible, and stable RNA interference in mammalian cells. Proc Natl Acad Sci U S A 2004; 101:1927-32. [PMID: 14762164 PMCID: PMC357029 DOI: 10.1073/pnas.0306111101] [Citation(s) in RCA: 169] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2003] [Indexed: 01/04/2023] Open
Abstract
RNA interference is a powerful genetic approach for efficiently silencing target genes. The existing method of gene suppression by the constitutive expression of short hairpin RNAs (shRNAs) allows analysis of the consequences of stably silencing genes but limits the analysis of genes essential for cell survival, cell cycle regulation, and cell development. We have developed an inducible U6 promoter for synthesis of shRNAs in both human and murine cells. Cells containing stably integrated shRNA expression constructs demonstrate stringent dosage- and time-dependent kinetics of induction with undetectable background expression in the absence of the inducer ecdysone. Inducible suppression of human p53 in glioblastoma cells shows striking morphological changes and defects in cell cycle arrest caused by DNA damage, as expected. Remarkably, the inducibility is reversible after withdrawal of the inducer, as observed by reappearance of the protein and a restoration of the original cell phenotype. Inducible and reversible regulation of RNA interference has broad applications in the areas of mammalian genetics and molecular therapeutics.
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Affiliation(s)
- Sunita Gupta
- Cancer Genome Research Center, Cold Spring Harbor Laboratory, 500 Sunnyside Boulevard, Woodbury, NY 11797, USA
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21
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Hinkley CS, Hirsch HA, Gu L, LaMere B, Henry RW. The small nuclear RNA-activating protein 190 Myb DNA binding domain stimulates TATA box-binding protein-TATA box recognition. J Biol Chem 2003; 278:18649-57. [PMID: 12621023 DOI: 10.1074/jbc.m204247200] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Human U6 small nuclear RNA (snRNA) gene transcription by RNA polymerase III requires cooperative promoter binding involving the snRNA-activating protein complex (SNAP(c)) and the TATA-box binding protein (TBP). To investigate the role of SNAP(c) for TBP function at U6 promoters, TBP recruitment assays were performed using full-length TBP and a mini-SNAP(c) containing SNAP43, SNAP50, and a truncated SNAP190. Mini-SNAP(c) efficiently recruits TBP to the U6 TATA box, and two SNAP(c) subunits, SNAP43 and SNAP190, directly interact with the TBP DNA binding domain. Truncated SNAP190 containing only the Myb DNA binding domain is sufficient for TBP recruitment to the TATA box. Therefore, the SNAP190 Myb domain functions both to specifically recognize the proximal sequence element present in the core promoters of human snRNA genes and to stimulate TBP recognition of the neighboring TATA box present in human U6 snRNA promoters. The SNAP190 Myb domain also stimulates complex assembly with TBP and Brf2, a subunit of a snRNA-specific TFIIIB complex. Thus, interactions between the DNA binding domains of SNAP190 and TBP at juxtaposed promoter elements define the assembly of a RNA polymerase III-specific preinitiation complex.
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Affiliation(s)
- Craig S Hinkley
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824, USA
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22
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Hovde S, Hinkley CS, Strong K, Brooks A, Gu L, Henry RW, Geiger J. Activator recruitment by the general transcription machinery: X-ray structural analysis of the Oct-1 POU domain/human U1 octamer/SNAP190 peptide ternary complex. Genes Dev 2002; 16:2772-7. [PMID: 12414730 PMCID: PMC187474 DOI: 10.1101/gad.1021002] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Transcriptional activation of the human U1 snRNA genes is dependent on a noncanonical octamer element contained within an upstream enhancer. The U1 octamer only weakly recruits the Oct-1 POU domain, although recruitment is stimulated by a peptide containing the Oct-1-binding domain of SNAP190. Structural analysis of the Oct-1 POU domain/U1 octamer/SNAP190 peptide complex revealed that SNAP190 makes extensive protein contacts with the Oct-1 POU-specific domain and with the DNA phosphate backbone within the enhancer. Although SNAP190 and OCA-B both interact with the Oct-1 POU domain through the same Oct-1 interface, a single nucleotide within the U1 octamer ablates OCA-B recruitment without compromising activator recruitment by SNAP190.
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Affiliation(s)
- Stacy Hovde
- Department of Chemistry, Michigan State University, East Lansing, Michigan 48823, USA
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23
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Nayak BK, Das GM. Stabilization of p53 and transactivation of its target genes in response to replication blockade. Oncogene 2002; 21:7226-9. [PMID: 12370812 DOI: 10.1038/sj.onc.1205889] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2002] [Revised: 07/12/2002] [Accepted: 07/18/2002] [Indexed: 11/08/2022]
Abstract
Although it is clear that p53 plays a pivotal role in G1/G2 checkpoints to conserve genomic integrity, its role in S phase checkpoint is less well understood. Recently, it has been reported that p53 is transcriptionally impaired even though it is stabilized during replication blockade. However, the mechanisms underlying this phenomenon are not known. In the present study, it has been shown that p53 accumulates and transactivates its target genes such as p21, gadd45 and bax in response to replication blockade in normal and cancer cells. Lack of transcriptional activation under similar conditions in cells lacking p53 shows that p53-target gene activation during replication blockade is indeed p53-dependent. Further, transactivation of p21 in response to replication blockade by hydroxyurea and aphidicolin is similar to that in response to ionizing radiation except that the latter is more immediate compared to the response to replication blockade. These findings suggest that impairment of transcriptionally active p53 in response to replication blockade is not a general phenomenon.
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Affiliation(s)
- Bijaya K Nayak
- Molecular Oncology Research Program, Department of Surgery, University of Texas Health Science Center, 7703 Floyd Curl Drive, San Antonio, Texas, TX 78229, USA
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24
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Affiliation(s)
- Laura Schramm
- Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
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25
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Arnosti DN. Design and function of transcriptional switches in Drosophila. INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY 2002; 32:1257-1273. [PMID: 12225917 DOI: 10.1016/s0965-1748(02)00089-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Extensive genetic and biochemical analysis of Drosophila melanogaster has made this system an important model for characterization of transcriptional regulatory elements and factors. Given the striking conservation of transcriptional controls in metazoans, general principles derived from studies of Drosophila are expected to continue to illuminate transcriptional regulation in other systems, including vertebrates. With improvement in technologies for genetic manipulation of insects, research in Drosophila will also aid the design of systems for controlled expression of genes in other hosts. This review focuses on recent advances from Drosophila in analysis of the functional components of transcriptional switches, including basal promoters, enhancers, boundary elements, and maintenance elements.
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Affiliation(s)
- D N Arnosti
- Michigan State University, Department of Biochemistry and Molecular Biology, East Lansing, MI 48824-1319, USA.
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26
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Li XY, Bhaumik SR, Zhu X, Li L, Shen WC, Dixit BL, Green MR. Selective recruitment of TAFs by yeast upstream activating sequences. Implications for eukaryotic promoter structure. Curr Biol 2002; 12:1240-4. [PMID: 12176335 DOI: 10.1016/s0960-9822(02)00932-6] [Citation(s) in RCA: 71] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The general transcription factor TFIID is composed of the TATA box binding protein (TBP) and multiple TBP-associated factors (TAFs). In yeast, promoters can be grouped into two classes based on the involvement of TAFs. TAF-dependent (TAF(dep)) promoters require TAFs for transcription, and TBP and TAFs are present at comparable levels on these promoters. TAF-independent (TAF(ind)) promoters do not require TAFs for activity, and TAFs are either absent or present at levels far below those of TBP on these promoters. Here, we demonstrate that the upstream activating sequence (UAS) mediates the selective recruitment of TAFs to TAF(dep) promoters. A TAF(ind) UAS fails to recruit TAFs and to direct efficient transcription when inserted upstream of a TAF(dep) core promoter. This transcriptional defect can be overcome by a potent activator, indicating that a strong activation domain can compensate for the absence of TAFs on a TAF(dep) core promoter. Our results reveal a requirement for compatibility between the UAS and core promoter and thus help explain previous reports that only certain yeast UAS-core promoter combinations and mammalian enhancer-promoter combinations are efficiently transcribed. The differential recruitment of TAFs by UASs provides strong evidence for the proposal that in vivo TAFs are the targets of some, but not all, activators.
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Affiliation(s)
- Xiao-Yong Li
- Howard Hughes Medical Institute, Programs in Gene Function and Expression and Molecular Medicine, University of Massachusetts Medical School, Worcester 01605, USA
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27
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Mach CM, Hargrove BW, Kunkel GR. The Small RNA gene activator protein, SphI postoctamer homology-binding factor/selenocysteine tRNA gene transcription activating factor, stimulates transcription of the human interferon regulatory factor-3 gene. J Biol Chem 2002; 277:4853-8. [PMID: 11724783 DOI: 10.1074/jbc.m108308200] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Many small nuclear RNA gene promoters are activated by SphI postoctamer homology (SPH)-binding factor/selenocysteine tRNA gene transcription activating factor (SBF/Staf). Whereas this transcription factor was initially identified by its ability to bind to SPH elements in such promoters, it was more recently shown to have the capacity to activate transcription of a synthetic mRNA gene promoter through a distinct activation domain. Here, we show that the human interferon regulatory factor-3 (IRF-3) gene promoter contains a functional SPH element that is bound by SBF/Staf in vitro and in transfected cells.
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Affiliation(s)
- Claire M Mach
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas 77843-2128, USA
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28
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Mansky KC, Marfatia K, Purdom GH, Luchin A, Hume DA, Ostrowski MC. The
microphthalmia
transcription factor (MITF) contains two N‐terminal domains required for transactivation of osteoclast target promoters and rescue of
mi
mutant osteoclasts. J Leukoc Biol 2002. [DOI: 10.1189/jlb.71.2.295] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Affiliation(s)
- Kim C. Mansky
- Departments of Microbiology and Biochemistry and the Centre for Molecular and Cellular Biology, University of Queensland, Brisbane, Australia
| | - Kavita Marfatia
- Departments of Microbiology and Biochemistry and the Centre for Molecular and Cellular Biology, University of Queensland, Brisbane, Australia
| | - Georgia H. Purdom
- Departments of Microbiology and Biochemistry and the Centre for Molecular and Cellular Biology, University of Queensland, Brisbane, Australia
| | - Alex Luchin
- Departments of Microbiology and Biochemistry and the Centre for Molecular and Cellular Biology, University of Queensland, Brisbane, Australia
| | - David A. Hume
- Departments of Microbiology and Biochemistry and the Centre for Molecular and Cellular Biology, University of Queensland, Brisbane, Australia
| | - Michael C. Ostrowski
- Departments of Microbiology and Biochemistry and the Centre for Molecular and Cellular Biology, University of Queensland, Brisbane, Australia
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29
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Hernandez N. Small nuclear RNA genes: a model system to study fundamental mechanisms of transcription. J Biol Chem 2001; 276:26733-6. [PMID: 11390411 DOI: 10.1074/jbc.r100032200] [Citation(s) in RCA: 181] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Affiliation(s)
- N Hernandez
- Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
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30
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Janody F, Sturny R, Schaeffer V, Azou Y, Dostatni N. Two distinct domains of Bicoid mediate its transcriptional downregulation by the Torso pathway. Development 2001; 128:2281-90. [PMID: 11493547 DOI: 10.1242/dev.128.12.2281] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The transcriptional activity of the Bicoid morphogen is directly downregulated by the Torso signal transduction cascade at the anterior pole of the Drosophila embryo. This regulation does not involve the homeodomain or direct phosphorylation of Bicoid. We analyse the transcriptional regulation of Bicoid in response to the Torso pathway, using Bicoid variants and fusion proteins between the Bicoid domains and the Gal4 DNA-binding domain. We show that Bicoid possesses three autonomous activation domains. Two of these domains, the serine/threonine-rich and the acidic domains, are downregulated by Torso, whereas the third activation domain, which is rich in glutamine, is not. The alanine-rich domain, previously described as an activation domain in vitro, has a repressive activity that is independent of Torso. Thus, Bicoid downregulation by Torso results from a competition between the glutamine-rich domain that is insensitive to Torso and the serine/threonine-rich and acidic activation domains downregulated by Torso. The alanine-rich domain contributes to this process indirectly by reducing the global activity of the protein and in particular the activity of the glutamine-rich domain that might otherwise prevent downregulation by Torso.
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Affiliation(s)
- F Janody
- Developmental Biology Institute of Marseille, Laboratoire de Génétique et Physiologie du Développement, Université de la Méditerrannée, Luminy, Case 907, 13288 Marseille Cedex 09, France
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31
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Corti C, Sala CF, Yang F, Corsi M, Xuereb JH, Ferraguti F. Genomic organization of the human metabotropic glutamate receptor subtype 3. J Neurogenet 2000; 14:207-25, 271. [PMID: 11342382 DOI: 10.3109/01677060009084499] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
In this study, the genomic organization of the human metabotropic glutamate receptor subtype 3 (mGluR3) gene has been determined. We have identified two transcription initiation sites and the polyadenylation signal by using 5'-rapid amplification of cDNA ends (RACE) and 3'-RACE, respectively. The exon/intron organization of the human mGluR3 gene revealed the presence of 6 exons separated by 5 introns. The size of introns varied from 10.4 to 120 kbp that contained consensus sequences for repetitive elements such as Alu and long interspersed elements. A putative promoter region flanking the 5' sequence of exon 1 was identified by computer-aided analysis. The putative promoter region was characterized by the presence of a CAAT and GC box, and the absence of a TATA box or CpG islands. Several putative binding sites for transcription factors were also identified. In addition, we have isolated, from a mouse genomic library, part of the mouse mGluR3 gene and found it to correspond to exon 2 in the human mGluR3 gene. The mouse mGluR3 gene was then mapped by fluorescent in situ hybridization analysis to chromosome 5qA2.
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MESH Headings
- Animals
- Base Sequence
- Chromosome Mapping
- Chromosomes, Human, Pair 7
- Data Interpretation, Statistical
- Electronic Data Processing
- Genomic Library
- Humans
- In Situ Hybridization, Fluorescence
- Mice
- Molecular Sequence Data
- Nucleic Acid Amplification Techniques
- Promoter Regions, Genetic
- RNA, Messenger/analysis
- Receptors, Metabotropic Glutamate/genetics
- Reverse Transcriptase Polymerase Chain Reaction
- Sequence Analysis, DNA
- Sequence Homology, Nucleic Acid
- Transcription, Genetic
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Affiliation(s)
- C Corti
- Biology Department, GlaxoWellcome Medicines Research Centre, Via Fleming 4, 37135 Verona, Italy
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32
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Wang Y, Dang J, Wang H, Allgayer H, Murrell GA, Boyd D. Identification of a novel nuclear factor-kappaB sequence involved in expression of urokinase-type plasminogen activator receptor. EUROPEAN JOURNAL OF BIOCHEMISTRY 2000; 267:3248-54. [PMID: 10824110 DOI: 10.1046/j.1432-1327.2000.01350.x] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
We have previously defined the promoter of human urokinase-type plasminogen activator receptor (uPAR) gene in a 188-bp fragment between bases -141 and +47 relative to the translation start site. Here, we report that a novel nuclear factor-kappaB (NF-kappaB)-like sequence (5'-GGGAGGAGTC-3') at -45 is located in the uPAR promoter and one of the two DNase I-protected regions, region I between bases -51 and -30. This NF-kappaB-like motif differs at positions 7-9 from the decameric consensus sequences of NF-kappaB (5'-GGGRNNYYCC-3' where R indicates A or G, Y indicates C or T, and N indicates any nucleotide) and at positions 1 and 7-9 from the kappaB-like motifs (5'-HGGARNYYCC-3' where H indicates A, C, or T, R indicates A or G, Y indicates C or T, and N indicates any nucleotide). Nuclear extracts from HCT116 cells contain proteins that specifically bind to the NF-kappaB-like site at position -45. Mutation of the NF-kappaB-like motif decreased the binding of transcription factor NF-kappaB and reduced the uPAR promoter activity in comparison with the wild-type sequences. Co-transfection with a dominant negative I-kappaB kinase-2 expression vector reduced uPAR promoter activity by 65-75%. These results demonstrate that a previously uncharacterized NF-kappaB motif is required for uPAR promoter activity.
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MESH Headings
- 5' Untranslated Regions/genetics
- Base Sequence
- Binding Sites/genetics
- Colonic Neoplasms/pathology
- Consensus Sequence
- DNA Footprinting
- Gene Expression Regulation
- Gene Expression Regulation, Neoplastic
- Genes, Reporter
- Humans
- I-kappa B Kinase
- Luciferases/biosynthesis
- Molecular Sequence Data
- NF-kappa B/physiology
- Promoter Regions, Genetic/genetics
- Protein Serine-Threonine Kinases/metabolism
- Receptors, Cell Surface/biosynthesis
- Receptors, Cell Surface/genetics
- Receptors, Urokinase Plasminogen Activator
- Recombinant Fusion Proteins/biosynthesis
- Recombinant Fusion Proteins/genetics
- Regulatory Sequences, Nucleic Acid
- Sequence Alignment
- Sequence Homology, Nucleic Acid
- Transcription, Genetic
- Transfection
- Tumor Cells, Cultured/metabolism
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Affiliation(s)
- Y Wang
- Division of Molecular Medicine, John Curtin School of Medical Research, The Australian National University, Canberra, Australia.
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33
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Knutson A, Castaño E, Oelgeschläger T, Roeder RG, Westin G. Downstream promoter sequences facilitate the formation of a specific transcription factor IID-promoter complex topology required for efficient transcription from the megalin/low density lipoprotein receptor-related protein 2 promoter. J Biol Chem 2000; 275:14190-7. [PMID: 10799495 DOI: 10.1074/jbc.275.19.14190] [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: 11/06/2022] Open
Abstract
Megalin/low density lipoprotein receptor-related protein 2 (LRP-2) is an endocytic receptor expressed in highly specialized cell types such as parathyroid cells and epithelia of the kidney. Previous experiments identified a nonconsensus TATA element, with the sequence TAGAAAA, as crucial for accurate and efficient transcription from the LRP-2 promoter. Here we show that, in addition to the TAGA element, promoter sequences downstream of the transcription start site contribute significantly to transcription both in vitro and in transfected cells. Deletion and point mutational analyses reveal that the promoter region located between positions +5 and +11 (sequence TTTTGGC) is of particular importance. Complementation experiments in nuclear extracts lacking transcription factor IID (TFIID) activity show that TATA-binding protein-associated factors of TFIID are essential for the function of LRP-2 downstream promoter sequences. Interestingly, DNase I footprinting studies show that the downstream region between positions +5 and +11 does not significantly affect overall TFIID affinity to the promoter but that it profoundly affects the topology of the TFIID x promoter complex not only downstream of the transcription start site, but in particular in the TATA box region. Our observations suggest a model for a novel downstream sequence function, in which TATA-binding protein-associated factor-promoter interactions downstream of the transcription start site modulate TFIID-DNA interactions in the TATA box region.
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Affiliation(s)
- A Knutson
- Department of Surgery, Endocrine Unit, Uppsala University Hospital, S-751 85 Uppsala, Sweden
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34
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Su PF, Chiang SY, Wu CW, Wu FY. Adeno-associated virus major Rep78 protein disrupts binding of TATA-binding protein to the p97 promoter of human papillomavirus type 16. J Virol 2000; 74:2459-65. [PMID: 10666281 PMCID: PMC111732 DOI: 10.1128/jvi.74.5.2459-2465.2000] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Adeno-associated virus type 2 (AAV) is known to inhibit the promoter activities of several oncogenes and viral genes, including the human papillomavirus type 16 (HPV-16) E6 and E7 transforming genes. However, the target elements of AAV on the long control region (LCR) upstream of E6 and E7 oncogenes are elusive. A chloramphenicol acetyltransferase assay was performed to study the effect of AAV on the transcription activity of the HPV-16 LCR in SiHa (HPV-positive) and C-33A (HPV-negative) cells. The results reveal that (i) AAV inhibited HPV-16 LCR activity in a dose-dependent manner, (ii) AAV-mediated inhibition did not require the HPV gene products, and (iii) the AAV replication gene product Rep78 was involved in the inhibition. Deletion mutation analyses of the HPV-16 LCR showed that regulatory elements outside the core promoter region of the LCR may not be direct targets of AAV-mediated inhibition. Further study with the electrophoretic mobility shift assay demonstrated that Rep78 interfered with the binding of TATA-binding protein (TBP) to the TATA box of the p97 core promoter more significantly than it disrupted the preformed TBP-TATA complex. These data thus suggest that Rep78 may inhibit transcription initiation of the HPV-16 LCR by disrupting the interaction between TBP and the TATA box of the p97 core promoter.
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Affiliation(s)
- P F Su
- Division of Cancer Research, Institute of Biomedical Sciences, Academia Sinica, Taiwan, Republic of China
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35
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Natesan S, Molinari E, Rivera VM, Rickles RJ, Gilman M. A general strategy to enhance the potency of chimeric transcriptional activators. Proc Natl Acad Sci U S A 1999; 96:13898-903. [PMID: 10570170 PMCID: PMC24162 DOI: 10.1073/pnas.96.24.13898] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Efforts to increase the potency of transcriptional activators are generally unsuccessful because poor expression of activators in mammalian cells limits their delivery to target promoters. Here we report that the effectiveness of chimeric activators can be dramatically improved by expressing them as noncovalent tetrameric bundles. Bundled activation domains are much more effective at activating a reporter gene than simple monomeric activators, presumably because, at similar expression levels, up to 4 times as many the activation domains are delivered to the target promoter. These bundled activation domains are also more effective than proteins in which activation domains are tandemly reiterated in the same polypeptide chain, because such proteins are very poorly expressed and therefore not delivered effectively. These observations suggest that there is a threshold number of activation domains that must be bound to a promoter for activation, above which promoter activity is simply a function of the number of activators bound. We show that bundling can be exploited practically to enhance the sensitivity of mammalian two-hybrid assays, enabling detection of weak interactions or those between poorly expressed proteins. Bundling also dramatically improves the performance of a small-molecule-regulated gene expression system when the expression level of regulatory protein is limiting, a situation that may be encountered in gene therapy applications.
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Affiliation(s)
- S Natesan
- ARIAD Gene Therapeutics Incorporated, 26 Landsdowne Street, Cambridge, MA 02139, USA.
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36
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Jordan R, Schang L, Schaffer PA. Transactivation of herpes simplex virus type 1 immediate-early gene expression by virion-associated factors is blocked by an inhibitor of cyclin-dependent protein kinases. J Virol 1999; 73:8843-7. [PMID: 10482641 PMCID: PMC112908 DOI: 10.1128/jvi.73.10.8843-8847.1999] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Initiation of productive infection by human herpes simplex virus type 1 (HSV-1) requires cell cycle-dependent protein kinase (cdk) activity. Treatment of cells with inhibitors of cdks blocks HSV-1 replication and prevents accumulation of viral transcripts, including immediate-early (IE) transcripts (26). Inhibition of IE transcript accumulation suggests that virion proteins, such as VP16, require functional cdks to activate viral transcription. In this report, we show that a cdk inhibitor, Roscovitine, blocks VP16-dependent IE gene expression. In the presence of Roscovitine, the level of virion-induced activation of a transfected reporter gene (the gene encoding chloramphenicol acetyltransferase) linked to the promoter-regulatory region of the ICP0 gene was reduced 40-fold relative to that of untreated samples. Roscovitine had little effect on the interaction of VP16 with VP16-responsive DNA sequences as measured by electrophoretic mobility shift assays. These data indicate that VP16-dependent activation of IE gene expression requires functional cdks and that this requirement is independent of the ability of VP16 to bind to DNA.
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Affiliation(s)
- R Jordan
- Department of Microbiology, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania 19104, USA.
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37
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Vance KW, Campo MS, Morgan IM. An enhanced epithelial response of a papillomavirus promoter to transcriptional activators. J Biol Chem 1999; 274:27839-44. [PMID: 10488130 DOI: 10.1074/jbc.274.39.27839] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Mucosal epitheliotropic papillomaviruses have a similar long control region (LCR) organization: a promoter region, an enhancer region, and a highly conserved distribution of E2 DNA binding sites. The enhancer of these viruses is epithelial-specific, as it fails to activate transcription from heterologous promoters in nonepithelial cell types (Gloss, B., Bernard, H. U., Seedorf, K., and Klock, G. (1987) EMBO J. 6, 3735-3743; Morgan, I. M., Grindlay, G. J., and Campo, M. S. (1999) J. Gen. Virol. 80, 23-27). Studies on E2 transcriptional regulation of the human mucosal epitheliotropic papillomaviruses have been hindered by poor access to the natural target cell type and by the observation that some of the human papillomavirus promoters, including human papillomavirus-16, are repressed in immortalized epithelial cells. Here we present results using the bovine papillomavirus-4 (BPV-4) LCR and a bovine primary cell system as a model to study the mechanism of E2 transcriptional regulation of mucosal epitheliotropic papillomaviruses and the cell type specificity of this regulation. E2 up-regulates transcription from the BPV-4 LCR preferentially in epithelial cells (Morgan, I. M., Grindlay, G. J., and Campo, M. S. (1998) J. Gen. Virol. 79, 501-508). We demonstrate that the epithelial-specific enhancer element of the BPV-4 LCR is not required for the enhanced activity of E2 in epithelial cells and that the BPV-4 promoter is more responsive, not only to E2, but to other transcriptional activators in epithelial cells. This is the first time a level of epithelial specificity has been shown to reside in a papillomavirus promoter region.
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Affiliation(s)
- K W Vance
- Beatson Institute for Cancer Research, Cancer Research Campaign Beatson Laboratories, Garscube Estate, Glasgow G61 1BD, Scotland
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38
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Senatore B, Cafieri A, Di Marino I, Rosati M, Di Nocera PP, Grimaldi G. A variety of RNA polymerases II and III-dependent promoter classes is repressed by factors containing the Krüppel-associated/finger preceding box of zinc finger proteins. Gene X 1999; 234:381-94. [PMID: 10395912 DOI: 10.1016/s0378-1119(99)00182-1] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
KRAB/FPB (Krüppel-associated/finger preceding box) domains are small, portable transcriptional repression motifs, encoded by hundreds of vertebrates C2-H2-type zinc finger genes. We report that KRAB/FPB domains feature an unprecedented, highly promiscuous DNA-binding dependent transcriptional repressing activity. Indeed, template bound chimeric factors containing KRAB/FPB modules actively repress in vivo the transcription of distinct promoter classes that depend on different core elements, recruit distinct basal transcriptional apparatuses and are transcribed either by RNA polymerase II or III. The promoter types repressed in transient assays in a dose- and DNA-binding dependent, but position- and orientation-independent manner, by GAL4-KRAB/FPB fusions include an RNA polymerase II-dependent small nuclear RNA promoter (U1) as well as RNA polymerase III-dependent class 2 (adenovirus VA1), class 3 (human U6) and atypical (human 7SL) promoters. Down-modulation of all of these templates depended on factors containing the A module of the KRAB/FPB domain. Data provide further insights into the properties and mode of action of this widespread repression motif, and support the notion that genes belonging to distinct classes may be repressed in vivo by KRAB/FPB containing zinc finger proteins. The exquisitely DNA-binding dependent transcriptional promiscuity exhibited by KRAB/FPB domains may provide a unique model system for studying the mechanism by which a promoter recruited repression motif can down-modulate a large variety of promoter types.
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Affiliation(s)
- B Senatore
- International Institute of Genetics and Biophysics, CNR, Via Marconi 10, Naples, Italy
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39
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Howcroft TK, Murphy C, Weissman JD, Huber SJ, Sawadogo M, Singer DS. Upstream stimulatory factor regulates major histocompatibility complex class I gene expression: the U2DeltaE4 splice variant abrogates E-box activity. Mol Cell Biol 1999; 19:4788-97. [PMID: 10373528 PMCID: PMC84277 DOI: 10.1128/mcb.19.7.4788] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/1999] [Accepted: 04/19/1999] [Indexed: 11/20/2022] Open
Abstract
The tissue-specific expression of major histocompatibility complex class I genes is determined by a series of upstream regulatory elements, many of which remain ill defined. We now report that a distal E-box element, located between bp -309 and -314 upstream of transcription initiation, acts as a cell type-specific enhancer of class I promoter activity. The class I E box is very active in a neuroblastoma cell line, CHP-126, but is relatively inactive in the HeLa epithelial cell line. The basic helix-loop-helix leucine zipper proteins upstream stimulatory factor 1 (USF1) and USF2 were shown to specifically recognize the class I E box, resulting in the activation of the downstream promoter. Fine mapping of USF1 and USF2 amino-terminal functional domains revealed differences in their abilities to activate the class I E box. Whereas USF1 contained only an extended activation domain, USF2 contained both an activation domain and a negative regulatory region. Surprisingly, the naturally occurring splice variant of USF2 lacking the exon 4 domain, U2DeltaE4, acted as a dominant-negative regulator of USF-mediated activation of the class I promoter. This latter activity is in sharp contrast to the known ability of U2DeltaE4 to activate the adenovirus major late promoter. Class I E-box function is correlated with the relative amount of U2DeltaE4 in a cell, leading to the proposal that U2DeltaE4 modulates class I E-box activity and may represent one mechanism to fine-tune class I expression in various tissues.
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Affiliation(s)
- T K Howcroft
- Experimental Immunology Branch, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892-1360, USA.
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40
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Herr W. The herpes simplex virus VP16-induced complex: mechanisms of combinatorial transcriptional regulation. COLD SPRING HARBOR SYMPOSIA ON QUANTITATIVE BIOLOGY 1999; 63:599-607. [PMID: 10384325 DOI: 10.1101/sqb.1998.63.599] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Affiliation(s)
- W Herr
- Cold Spring Harbor Laboratory, New York 11724, USA
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41
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Henry RW, Ford E, Mital R, Mittal V, Hernandez N. Crossing the line between RNA polymerases: transcription of human snRNA genes by RNA polymerases II and III. COLD SPRING HARBOR SYMPOSIA ON QUANTITATIVE BIOLOGY 1999; 63:111-20. [PMID: 10384275 DOI: 10.1101/sqb.1998.63.111] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Affiliation(s)
- R W Henry
- Cold Spring Harbor Laboratory, New York 11724, USA
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42
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Shen WC, Apone LM, Virbasius CM, Li XY, Monsalve M, Green MR. Functional analysis of TFIID components. COLD SPRING HARBOR SYMPOSIA ON QUANTITATIVE BIOLOGY 1999; 63:219-27. [PMID: 10384285 DOI: 10.1101/sqb.1998.63.219] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Affiliation(s)
- W C Shen
- Howard Hughes Medical Institute, Program in Molecular Medicine, University of Massachusetts Medical Center, Worcester 01605, USA
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43
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Fry CJ, Pearson A, Malinowski E, Bartley SM, Greenblatt J, Farnham PJ. Activation of the murine dihydrofolate reductase promoter by E2F1. A requirement for CBP recruitment. J Biol Chem 1999; 274:15883-91. [PMID: 10336493 DOI: 10.1074/jbc.274.22.15883] [Citation(s) in RCA: 45] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The E2F family of heterodimeric transcription factors plays an important role in the regulation of gene expression at the G1/S phase transition of the mammalian cell cycle. Previously, we have demonstrated that cell cycle regulation of murine dihydrofolate reductase (dhfr) expression requires E2F-mediated activation of the dhfr promoter in S phase. To investigate the mechanism by which E2F activates an authentic E2F-regulated promoter, we precisely replaced the E2F binding site in the dhfr promoter with a Gal4 binding site. Using Gal4-E2F1 derivatives, we found that E2F1 amino acids 409-437 contain a potent core transactivation domain. Functional analysis of the E2F1 core domain demonstrated that replacement of phenylalanine residues 413, 425, and 429 with alanine reduces both transcriptional activation of the dhfr promoter and protein-protein interactions with CBP, transcription factor (TF) IIH, and TATA-binding protein (TBP). However, additional amino acid substitutions for phenylalanine 429 demonstrated a strong correlation between activation of the dhfr promoter and binding of CBP, but not TFIIH or TBP. Finally, transactivator bypass experiments indicated that direct recruitment of CBP is sufficient for activation of the dhfr promoter. Therefore, we suggest that recruitment of CBP is one mechanism by which E2F activates the dhfr promoter.
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Affiliation(s)
- C J Fry
- McArdle Laboratory for Cancer Research, University of Wisconsin Medical School, Madison, Wisconsin 53706, USA
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44
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Stagljar I, Hübscher U, Barberis A. Activation of DNA replication in yeast by recruitment of the RNA polymerase II transcription complex. Biol Chem 1999; 380:525-30. [PMID: 10384958 DOI: 10.1515/bc.1999.067] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Activators of transcription are known to also play an important and direct role in activating DNA replication. However, the mechanism whereby they stimulate replication has remained elusive. One model suggests that, in the context of replication origins, transcriptional activators work by interacting with replication factors. We show that a defined, single interaction between a DNA-bound derivative of the activator Gal4 and Gal11P, a mutant form of the RNA polymerase II holoenzyme component Gal11, suffices for stimulating DNA replication as it does for transcription. Moreover, recruitment of TBP, which can activate transcription from a gene promoter, also stimulates DNA replication from an origin site. These results strongly argue that transcriptional activators may not necessarily need to contact DNA replication factors directly, but can stimulate replication by recruiting the RNA polymerase II transcription complex to DNA.
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Affiliation(s)
- I Stagljar
- Institute for Veterinary Biochemistry, University of Zürich, Switzerland
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45
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Salghetti SE, Kim SY, Tansey WP. Destruction of Myc by ubiquitin-mediated proteolysis: cancer-associated and transforming mutations stabilize Myc. EMBO J 1999; 18:717-26. [PMID: 9927431 PMCID: PMC1171164 DOI: 10.1093/emboj/18.3.717] [Citation(s) in RCA: 352] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The human proto-oncogene c-myc encodes a highly unstable transcription factor that promotes cell proliferation. Although the extreme instability of Myc plays an important role in preventing its accumulation in normal cells, little is known about how Myc is targeted for rapid destruction. Here, we have investigated mechanisms regulating the stability of Myc. We show that Myc is destroyed by ubiquitin-mediated proteolysis, and define two elements in Myc that oppositely regulate its stability: a transcriptional activation domain that promotes Myc destruction, and a region required for association with the POZ domain protein Miz-1 that stabilizes Myc. We also show that Myc is stabilized by cancer-associated and transforming mutations within its transcriptional activation domain. Our data reveal a complex network of interactions regulating Myc destruction, and imply that enhanced protein stability contributes to oncogenic transformation by mutant Myc proteins.
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Affiliation(s)
- S E Salghetti
- Cold Spring Harbor Laboratory, 1 Bungtown Road, PO Box 100, Cold Spring Harbor, NY 11724, USA
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46
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Barberis A, Gaudreau L. Recruitment of the RNA polymerase II holoenzyme and its implications in gene regulation. Biol Chem 1998; 379:1397-405. [PMID: 9894806 DOI: 10.1515/bchm.1998.379.12.1397] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
In yeast cells, interaction between a DNA-bound protein and a single component of the RNA polymerase II (poIII) holoenzyme is sufficient to recruit the latter to a promoter and thereby activate gene transcription. Here we review results which have suggested such a simple mechanism for how genes can be turned on. The series of experiments which eventually led to this model was originally instigated by studying gene expression in a yeast strain which carries a point mutation in Gal11, a component of the poIII holoenzyme. In cells containing this mutant protein termed Gall11P, a derivative of the transcriptional activator Gal4 devoid of any classical activating region is turned into a strong activator. This activating function acquired by an otherwise silent DNA-binding protein is solely due to a novel and fortuitous interaction between Gal11P and a fragment of the Gal4 dimerization region generated by the P mutation. The simplest explanation for these results is that tethering Gal11 to DNA recruits the poIII holoenzyme and, consequently, activates gene transcription. Transcription factors that are believed not to be integral part of the poIII holoenzyme but are nevertheless required for this instance of gene activation, e.g. the TATA-binding TFIID complex, may bind DNA cooperatively with the holoenzyme when recruited to a promoter, thus forming a complete poIII preinitiation complex. One prediction of this model is that recruitment of the entire poIII transcription complex and consequent gene activation can be achieved by tethering different components to DNA. Indeed, fusion of a DNA-binding domain to a variety of poIII holoenzyme components and TFIID subunits leads to activation of genes bearing the recognition site for the DNA-binding protein. These results imply that accessory factors, which are required to remove or modify nucleosomes do not need to be directly contacted by activators, but can rather be engaged in the activation process when the poIII complex is recruited to DNA. In fact, recruitment of the poIII holoenzyme suffices to remodel nucleosomes at the PHO5 promoter and presumably at many other promoters. Other events in the process of gene expression following recruitment of the transcription complex, e.g. initiation, promoter clearance, elongation and termination, could unravel as a consequence of the recruitment step and the formation of an active preinitiation complex on DNA. This view does not exclude the possibility that classical activators also act directly on chromatin remodeling and post-recruitment steps to regulate gene expression.
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Affiliation(s)
- A Barberis
- Institute of Molecular Biology, University of Zurich, Switzerland
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47
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Folkers GE, van der Burg B, van der Saag PT. Promoter architecture, cofactors, and orphan receptors contribute to cell-specific activation of the retinoic acid receptor beta2 promoter. J Biol Chem 1998; 273:32200-12. [PMID: 9822698 DOI: 10.1074/jbc.273.48.32200] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Expression of retinoic acid receptor beta (RARbeta) is spatially and temporally restricted during embryonal development. Also during retinoic acid (RA)-dependent embryonal carcinoma (EC) cell differentiation, RARbeta expression is initially up-regulated, while in later phases of differentiation expression is down-regulated, by an unknown mechanism. To gain insight into the regulation of RARbeta, we studied the activity of the RARbeta2 promoter and mutants thereof in various cell lines. While the RARbeta2 promoter is activated by RA in a limited number of cell lines, synthetic RA-responsive reporters are activated in most cell types. We show that the expression levels of proteins that bind to the beta-retinoic acid response element (RAR/retinoid X receptors and orphan receptors) and also the differential expression of a number of coactivators modulate the RA response on both natural and synthetic reporters. We further show that cell type-specific activation of the RARbeta2 promoter is dependent on the promoter architecture including the spacing between retinoic acid response element and TATA-box and initiator sequence (betaINR). Mutation within these regions caused a decrease in the activity of this promoter in responsive EC cells, while an increase in activity in non-EC cell lines was observed. Cell-specific complexes were formed on the betaINR, suggesting that the betaINR contributes to cell-specific activation of the promoter. On this basis we propose that promoter context-dependent and more general RA response-determining mechanisms contribute to cell-specific RA-dependent activation of transcription.
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Affiliation(s)
- G E Folkers
- Hubrecht Laboratory, Netherlands Institute for Developmental Biology, 3584 CH Utrecht, The Netherlands
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48
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Ford E, Strubin M, Hernandez N. The Oct-1 POU domain activates snRNA gene transcription by contacting a region in the SNAPc largest subunit that bears sequence similarities to the Oct-1 coactivator OBF-1. Genes Dev 1998; 12:3528-40. [PMID: 9832505 PMCID: PMC317248 DOI: 10.1101/gad.12.22.3528] [Citation(s) in RCA: 48] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/1998] [Accepted: 09/29/1998] [Indexed: 11/24/2022]
Abstract
The RNA polymerases II and III snRNA gene promoters contain an octamer sequence as part of the enhancer and a proximal sequence element (PSE) as part of the core promoter. The octamer and the PSE bind the POU domain activator Oct-1 and the basal transcription factor SNAPc, respectively. Oct-1, but not Oct-1 with a single E7R mutation within the POU domain, binds cooperatively with SNAPc and, in effect, recruits SNAPc to the PSE. Here, we show that SNAPc recruitment is mediated by an interaction between the Oct-1 POU domain and a small region of the largest subunit of SNAPc, SNAP190. This SNAP190 region is strikingly similar to a region in the B-cell-specific Oct-1 coactivator, OBF-1, that is required for interaction with octamer-bound Oct-1 POU domain. The Oct-1 POU domain-SNAP190 interaction is a direct protein-protein contact as determined by the isolation of a switched specificity SNAP190 mutant that interacts with Oct-1 POU E7R but not with wild-type Oct-1 POU. We also show that this direct protein-protein contact results in activation of transcription. Thus, we have identified an activation target of a human activator, Oct-1, within its cognate basal transcription complex.
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Affiliation(s)
- E Ford
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724 USA
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49
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Martinez E, Ge H, Tao Y, Yuan CX, Palhan V, Roeder RG. Novel cofactors and TFIIA mediate functional core promoter selectivity by the human TAFII150-containing TFIID complex. Mol Cell Biol 1998; 18:6571-83. [PMID: 9774672 PMCID: PMC109242 DOI: 10.1128/mcb.18.11.6571] [Citation(s) in RCA: 59] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/1998] [Accepted: 07/31/1998] [Indexed: 12/17/2022] Open
Abstract
TATA-binding protein-associated factors (TAFIIs) within TFIID control differential gene transcription through interactions with both activators and core promoter elements. In particular, TAFII150 contributes to initiator-dependent transcription through an unknown mechanism. Here, we address whether TAFIIs within TFIID are sufficient, in conjunction with highly purified general transcription factors (GTFs), for differential core promoter-dependent transcription by RNA polymerase II and whether additional cofactors are required. We identify the human homologue of Drosophila TAFII150 through cognate cDNA cloning and show that it is a tightly associated component of human TFIID. More importantly, we demonstrate that the human TAFII150-containing TFIID complex is not sufficient, in the context of all purified GTFs and RNA polymerase II, to mediate transcription synergism between TATA and initiator elements and initiator-directed transcription from a TAFII-dependent TATA-less promoter. Therefore, TAFII-promoter interactions are not sufficient for the productive core promoter-selective functions of TFIID. Consistent with this finding, we have partially purified novel cofactor activities (TICs) that potentiate the TAFII-mediated synergism between TATA and initiator elements (TIC-1) and TAFII-dependent transcription from TATA-less promoters (TIC-2 and -3). Furthermore, we demonstrate an essential function for TFIIA in TIC- and TAFII-dependent basal transcription from a TATA-less promoter. Our results reveal a parallel between the basal transcription activity of TAFIIs through core promoter elements and TAFII-dependent activator function.
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Affiliation(s)
- E Martinez
- Laboratory of Biochemistry and Molecular Biology, The Rockefeller University, New York, New York 10021, USA
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50
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Song YH, Ray K, Liebhaber SA, Cooke NE. Vitamin D-binding protein gene transcription is regulated by the relative abundance of hepatocyte nuclear factors 1alpha and 1beta. J Biol Chem 1998; 273:28408-18. [PMID: 9774468 DOI: 10.1074/jbc.273.43.28408] [Citation(s) in RCA: 41] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Vitamin D-binding protein (DBP)/Gc-globulin, the major carrier of vitamin D and its metabolites in blood, is synthesized predominantly in the liver in a developmentally regulated fashion. By transient transfection analysis, we identified three regions in the 5'-flanking region of the rat DBP gene, segments F-2, B, and A, that contain tissue-specific transcriptional determinants. Gel mobility shift and DNase I footprinting analyses showed that all three regions contained binding sites for the hepatocyte nuclear factor 1 (HNF1), a transcriptional regulator composed of HNF1alpha and HNF1beta hetero- and homodimers. The activity of the most proximal segment A (coordinates -141 to -43) was DBP promoter-specific, position-dependent, and positively controlled by HNF1alpha. In contrast, the two more distal determinants (segments F-2 and B; coordinates -1844 to -1621 and -254 to -140, respectively) acted as classical enhancers in transfected hepatocyte-derived HepG2 cells; their activities were promoter- and orientation-independent, and disruption of their respective HNF1-binding sites resulted in marked loss of DBP gene expression. Remarkably, the activities of these two distal elements depended upon the relative levels of HNF1alpha and HNF1beta; HNF1alpha had a major stimulatory effect, whereas HNF1beta acted as a trans-dominant inhibitor of HNF1alpha-mediated enhancer activity. These results suggested that the net expression of the DBP gene reflected a balance between the two major HNF1 species; the relative abundance of HNF1alpha and HNF1beta proteins in a cell may thus play a critical role in determining the pattern of gene expression.
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Affiliation(s)
- Y H Song
- Departments of Medicine and Genetics, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
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