1
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Jiménez-Mejía G, Montalvo-Méndez R, Hernández-Bautista C, Altamirano-Torres C, Vázquez M, Zurita M, Reséndez-Pérez D. Trimeric complexes of Antp-TBP with TFIIEβ or Exd modulate transcriptional activity. Hereditas 2022; 159:23. [PMID: 35637493 PMCID: PMC9150345 DOI: 10.1186/s41065-022-00239-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Accepted: 05/17/2022] [Indexed: 11/10/2022] Open
Abstract
Background Hox proteins finely coordinate antero-posterior axis during embryonic development and through their action specific target genes are expressed at the right time and space to determine the embryo body plan. As master transcriptional regulators, Hox proteins recognize DNA through the homeodomain (HD) and interact with a multitude of proteins, including general transcription factors and other cofactors. HD binding specificity increases by protein–protein interactions with a diversity of cofactors that outline the Hox interactome and determine the transcriptional landscape of the selected target genes. All these interactions clearly demonstrate Hox-driven transcriptional regulation, but its precise mechanism remains to be elucidated. Results Here we report Antennapedia (Antp) Hox protein–protein interaction with the TATA-binding protein (TBP) and the formation of novel trimeric complexes with TFIIEβ and Extradenticle (Exd), as well as its participation in transcriptional regulation. Using Bimolecular Fluorescence Complementation (BiFC), we detected the interaction of Antp-TBP and, in combination with Förster Resonance Energy Transfer (BiFC-FRET), the formation of the trimeric complex with TFIIEβ and Exd in living cells. Mutational analysis showed that Antp interacts with TBP through their N-terminal polyglutamine-stretches. The trimeric complexes of Antp-TBP with TFIIEβ and Exd were validated using different Antp mutations to disrupt the trimeric complexes. Interestingly, the trimeric complex Antp-TBP-TFIIEβ significantly increased the transcriptional activity of Antp, whereas Exd diminished its transactivation. Conclusions Our findings provide important insights into the Antp interactome with the direct interaction of Antp with TBP and the two new trimeric complexes with TFIIEβ and Exd. These novel interactions open the possibility to analyze promoter function and gene expression to measure transcription factor binding dynamics at target sites throughout the genome. Supplementary Information The online version contains supplementary material available at 10.1186/s41065-022-00239-8.
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Osman NM, Kitapci TH, Vlaho S, Wunderlich Z, Nuzhdin SV. Inference of Transcription Factor Regulation Patterns Using Gene Expression Covariation in Natural Populations of Drosophila melanogaster. Biophysics (Nagoya-shi) 2019; 63:43-51. [PMID: 30739944 DOI: 10.1134/s0006350918010128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Gene regulatory networks control the complex programs that drive development. Deciphering the connections between transcription factors (TFs) and target genes is challenging, in part because TFs bind to thousands of places in the genome but control expression through a subset of these binding events. We hypothesize that we can combine natural variation of expression levels and predictions of TF binding sites to identify TF targets. We gather RNA-seq data from 71 genetically distinct F1 Drosophila melanogaster embryos and calculate the correlations between TF and potential target genes' expression levels, which we call "regulatory strength." To separate direct and indirect TF targets, we hypothesize that direct TF targets will have a preponderance of binding sites in their upstream regions. Using 14 TFs active during embryogenesis, we find that 12 TFs showed a significant correlation between their binding strength and regulatory strength on downstream targets, and 10 TFs showed a significant correlation between the number of binding sites and the regulatory effect on target genes. The general roles, e.g. bicoid's role as an activator, and the particular interactions we observed between our TFs, e.g. twist's role as a repressor of sloppy paired and odd paired, generally coincide with the literature.
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Affiliation(s)
- Noha M Osman
- University of Southern California, Los Angeles, CA.,National Research Centre, Dokki, Giza, Egypt
| | | | - Srna Vlaho
- University of Southern California, Los Angeles, CA
| | | | - Sergey V Nuzhdin
- University of Southern California, Los Angeles, CA.,Saint Petersburg Polytechnical University, St Petersburg, Russia
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3
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Altamirano-Torres C, Salinas-Hernández JE, Cárdenas-Chávez DL, Rodríguez-Padilla C, Reséndez-Pérez D. Transcription factor TFIIEβ interacts with two exposed positions in helix 2 of the Antennapedia homeodomain to control homeotic function in Drosophila. PLoS One 2018; 13:e0205905. [PMID: 30321227 PMCID: PMC6188894 DOI: 10.1371/journal.pone.0205905] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Accepted: 10/03/2018] [Indexed: 01/02/2023] Open
Abstract
Homeoproteins contain the conserved homeodomain (HD) and have an important role determining embryo body plan during development. HDs increase their DNA-binding specificity by interacting with additional cofactors outlining a Hox interactome with a multiplicity of protein-protein interactions. In Drosophila, the first link of functional contact with a general transcription factor (GTF) was found between Antennapedia (Antp) and BIP2 (TFIID complex). Hox proteins also interact with other components of Pol II machinery such as the subunit Med19 from Mediator (MED) complex, TFIIEβ and transcription-pausing factor M1BP. All these interactions clearly demonstrate Hox-driven transcriptional regulation, but the precise molecular mechanism remains unclear. In this paper, we focused on the Antp-TFIIEβ protein-protein interface to establish the specific contacts as well as its functional role. Using Bimolecular Fluorescence Complementation (BiFC) in cell culture and in vivo we found that TFIIEβ interacts with Antp through the HD independently of the YPWM motif and the direct physical interaction is at helix 2, specifically aminoacidic positions I32 and H36 of Antp. We also found, through ectopic assays, that these two positions in helix 2 are crucial for Antp homeotic function in head involution, and thoracic and antenna-to tarsus transformations. Interestingly, overexpression of Antp and TFIIEβ in the antennal disc showed that this interaction is required for the antenna-to-tarsus transformation. In conclusion, interaction of Antp with TFIIEβ is important for the functional specificity of Antennapedia, and amino acids 32 and 36 in Antp HD helix 2 are key for this interaction. Our results open the possibility to more broadly analyze Antp-TFIIEβ interaction on the transcriptional control for the activation and/or repression of target genes in the Hox interactome during Drosophila development.
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Affiliation(s)
- Claudia Altamirano-Torres
- Department of Immunology and Virology, College of Biological Sciences, Universidad Autónoma de Nuevo León, San Nicolás de los Garza, Nuevo León, México
- Department of Cell Biology and Genetics, College of Biological Sciences, Universidad Autónoma de Nuevo León, San Nicolás de los Garza, Nuevo León, México
| | - Jannet E. Salinas-Hernández
- Department of Immunology and Virology, College of Biological Sciences, Universidad Autónoma de Nuevo León, San Nicolás de los Garza, Nuevo León, México
| | - Diana L. Cárdenas-Chávez
- Department of Immunology and Virology, College of Biological Sciences, Universidad Autónoma de Nuevo León, San Nicolás de los Garza, Nuevo León, México
| | - Cristina Rodríguez-Padilla
- Department of Immunology and Virology, College of Biological Sciences, Universidad Autónoma de Nuevo León, San Nicolás de los Garza, Nuevo León, México
| | - Diana Reséndez-Pérez
- Department of Immunology and Virology, College of Biological Sciences, Universidad Autónoma de Nuevo León, San Nicolás de los Garza, Nuevo León, México
- Department of Cell Biology and Genetics, College of Biological Sciences, Universidad Autónoma de Nuevo León, San Nicolás de los Garza, Nuevo León, México
- * E-mail:
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4
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Müller Glia Cells Activation in Rat Retina After Optic Nerve Injury: Spatiotemporal Correlation with Transcription Initiation Factor IIB. J Mol Neurosci 2013; 51:37-46. [DOI: 10.1007/s12031-012-9941-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2012] [Accepted: 11/21/2012] [Indexed: 10/27/2022]
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5
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Sang A, Xu Y, Jin N, Zhou T, Wang J, Zhu J, Chen C, Shi J, Shuai J, Xu G, Gu Z. Involvement of transcription initiation factor IIB in the light-induced death of rat retinal ganglion cells in vivo. J Mol Histol 2012; 44:11-8. [PMID: 23264107 DOI: 10.1007/s10735-012-9446-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2012] [Accepted: 08/16/2012] [Indexed: 12/16/2022]
Abstract
Transcription initiation factor IIB (TFIIB) is a general transcription initiation factor that plays a pivotal role in the response to transcriptional activator proteins. Previous reports have shown that TFIIB have been implicated in the pathogenesis of various experimental central nervous system diseases. However, its distribution and function in the retina remain unclear. In the present study, we investigated the spatiotemporal expression of TFIIB in a light-induced retinal damage model. Western blotting analysis showed TFIIB level significantly improved 3 days after injury, and then declined during the following days. The association of TFIIB and retinal ganglion cells (RGCs) was detected by immunofluorescence double staining. The injury-induced expression of TFIIB was physically co-existed with active caspase-3 and TUNEL (apoptotic markers). Spatiotemporal changes of TFIIB expression suggest that this protein may play a role in the degenerative process of RGCs by light-induced damage in the retina.
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Affiliation(s)
- Aimin Sang
- Department of Ophthalmology, Affiliated Hospital of Nantong University, Nantong, Jiangsu Province, People's Republic of China
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6
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Thermodynamics-based models of transcriptional regulation by enhancers: the roles of synergistic activation, cooperative binding and short-range repression. PLoS Comput Biol 2010; 6. [PMID: 20862354 PMCID: PMC2940721 DOI: 10.1371/journal.pcbi.1000935] [Citation(s) in RCA: 123] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2010] [Accepted: 08/17/2010] [Indexed: 01/08/2023] Open
Abstract
Quantitative models of cis-regulatory activity have the potential to improve our mechanistic understanding of transcriptional regulation. However, the few models available today have been based on simplistic assumptions about the sequences being modeled, or heuristic approximations of the underlying regulatory mechanisms. We have developed a thermodynamics-based model to predict gene expression driven by any DNA sequence, as a function of transcription factor concentrations and their DNA-binding specificities. It uses statistical thermodynamics theory to model not only protein-DNA interaction, but also the effect of DNA-bound activators and repressors on gene expression. In addition, the model incorporates mechanistic features such as synergistic effect of multiple activators, short range repression, and cooperativity in transcription factor-DNA binding, allowing us to systematically evaluate the significance of these features in the context of available expression data. Using this model on segmentation-related enhancers in Drosophila, we find that transcriptional synergy due to simultaneous action of multiple activators helps explain the data beyond what can be explained by cooperative DNA-binding alone. We find clear support for the phenomenon of short-range repression, where repressors do not directly interact with the basal transcriptional machinery. We also find that the binding sites contributing to an enhancer's function may not be conserved during evolution, and a noticeable fraction of these undergo lineage-specific changes. Our implementation of the model, called GEMSTAT, is the first publicly available program for simultaneously modeling the regulatory activities of a given set of sequences. The development of complex multicellular organisms requires genes to be expressed at specific stages and in specific tissues. Regulatory DNA sequences, often called cis-regulatory modules, drive the desired gene expression patterns by integrating information about the environment in the form of the activities of transcription factors. The rules by which regulatory sequences read this type of information, however, are unclear. In this work, we developed quantitative models based on physicochemical principles that directly map regulatory sequences to the expression profiles they generate. We evaluated these models on the segmentation network of the model organism Drosophila melanogaster. Our models incorporate mechanistic features that attempt to capture how activating and repressing transcription factors work in the segmentation system. By evaluating the importance of these features, we were able to gain insights on the quantitative regulatory rules. We found that two different mechanisms may contribute to cooperative gene activation and that repressors often have a short range of influence in DNA sequences. Combining the quantitative modeling with comparative sequence analysis, we also found that even functional sequences may be lost during evolution.
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7
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Deng W, Roberts SGE. TFIIB and the regulation of transcription by RNA polymerase II. Chromosoma 2007; 116:417-29. [PMID: 17593382 DOI: 10.1007/s00412-007-0113-9] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2007] [Revised: 05/21/2007] [Accepted: 05/21/2007] [Indexed: 02/01/2023]
Abstract
Accurate transcription of a gene by RNA polymerase II requires the assembly of a group of general transcription factors at the promoter. The general transcription factor TFIIB plays a central role in preinitiation complex assembly, providing a bridge between promoter-bound TFIID and RNA polymerase II. TFIIB makes extensive contact with the core promoter via two independent DNA-recognition modules. In addition to interacting with other general transcription factors, TFIIB directly modulates the catalytic center of RNA polymerase II in the transcription complex. Moreover, TFIIB has been proposed as a target of transcriptional activator proteins that act to stimulate preinitiation complex assembly. In this review, we will discuss our current understanding of these activities of TFIIB.
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Affiliation(s)
- Wensheng Deng
- Faculty of Life Sciences, University of Manchester, The Michael Smith Building, Oxford Road, Manchester, M13 9PT, UK
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8
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Shi H, Fan X, Sevilimedu A, Lis JT. RNA aptamers directed to discrete functional sites on a single protein structural domain. Proc Natl Acad Sci U S A 2007; 104:3742-6. [PMID: 17360423 PMCID: PMC1820654 DOI: 10.1073/pnas.0607805104] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2006] [Indexed: 11/18/2022] Open
Abstract
Cellular regulatory networks are organized such that many proteins have few interactions, whereas a few proteins have many. These densely connected protein "hubs" are critical for the system-wide behavior of cells, and the capability of selectively perturbing a subset of interactions at these hubs is invaluable in deciphering and manipulating regulatory mechanisms. SELEX-generated RNA aptamers are proving to be highly effective reagents for inhibiting targeted proteins, but conventional methods generate one or several aptamer clones that usually bind to a single target site most preferred by a nucleic acid ligand. We advance a generalized scheme for isolating aptamers to multiple sites on a target molecule by reducing the ability of the preferred site to select its cognate aptamer. We demonstrate the use of this scheme by generating aptamers directed to discrete functional surfaces of the yeast TATA-binding protein (TBP). Previously we selected "class 1" RNA aptamers that interfere with the TBP's binding to TATA-DNA. By masking TBP with TATA-DNA or an unamplifiable class 1 aptamer, we isolated a new aptamer class, "class 2," that can bind a TBP.DNA complex and is in competition with binding another general transcription factor, TFIIA. Moreover, we show that both of these aptamers inhibit RNA polymerase II-dependent transcription, but analysis of template-bound factors shows they do so in mechanistically distinct and unexpected ways that can be attributed to binding either the DNA or TFIIA recognition sites. These results should spur innovative approaches to modulating other highly connected regulatory proteins.
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Affiliation(s)
- Hua Shi
- *Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853; and
- Department of Biological Sciences, University at Albany, State University of New York, Albany, NY 12222
| | - Xiaochun Fan
- *Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853; and
| | - Aarti Sevilimedu
- *Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853; and
| | - John T. Lis
- *Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853; and
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9
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Zanton SJ, Pugh BF. Full and partial genome-wide assembly and disassembly of the yeast transcription machinery in response to heat shock. Genes Dev 2006; 20:2250-65. [PMID: 16912275 PMCID: PMC1553208 DOI: 10.1101/gad.1437506] [Citation(s) in RCA: 89] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Eukaryotic genes are controlled by sequence-specific DNA-binding proteins, chromatin regulators, general transcription factors, and elongation factors. Here we examine the genome-wide location of representative members of these groups and their redistribution when the Saccharomyces cerevisiae genome is reprogrammed by heat shock. As expected, assembly of active transcription complexes is coupled to eviction of H2A.Z nucleosomes, and disassembly is coupled to the return of nucleosomes. Remarkably, a large number of promoters assemble into partial preinitiation complexes (partial PICs), containing TFIIA, TFIID (and/or SAGA), TFIIB, TFIIE, and TFIIF. However, RNA polymerase II and TFIIH are generally not recruited, and nucleosomes are not displaced. These promoters may be preparing for additional stress that naturally accompany heat stress. For example, we find that oxidative stress, which often occurs with prolonged exposure of cells to high temperature, converts partial PICs into full PICs. Partial PICs therefore represent novel regulated intermediates that assemble at promoters in the midst of chromatin.
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Affiliation(s)
- Sara J Zanton
- Center for Gene Regulation, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
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10
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Abstract
In eukaryotes, the core promoter serves as a platform for the assembly of transcription preinitiation complex (PIC) that includes TFIIA, TFIIB, TFIID, TFIIE, TFIIF, TFIIH, and RNA polymerase II (pol II), which function collectively to specify the transcription start site. PIC formation usually begins with TFIID binding to the TATA box, initiator, and/or downstream promoter element (DPE) found in most core promoters, followed by the entry of other general transcription factors (GTFs) and pol II through either a sequential assembly or a preassembled pol II holoenzyme pathway. Formation of this promoter-bound complex is sufficient for a basal level of transcription. However, for activator-dependent (or regulated) transcription, general cofactors are often required to transmit regulatory signals between gene-specific activators and the general transcription machinery. Three classes of general cofactors, including TBP-associated factors (TAFs), Mediator, and upstream stimulatory activity (USA)-derived positive cofactors (PC1/PARP-1, PC2, PC3/DNA topoisomerase I, and PC4) and negative cofactor 1 (NC1/HMGB1), normally function independently or in combination to fine-tune the promoter activity in a gene-specific or cell-type-specific manner. In addition, other cofactors, such as TAF1, BTAF1, and negative cofactor 2 (NC2), can also modulate TBP or TFIID binding to the core promoter. In general, these cofactors are capable of repressing basal transcription when activators are absent and stimulating transcription in the presence of activators. Here we review the roles of these cofactors and GTFs, as well as TBP-related factors (TRFs), TAF-containing complexes (TFTC, SAGA, SLIK/SALSA, STAGA, and PRC1) and TAF variants, in pol II-mediated transcription, with emphasis on the events occurring after the chromatin has been remodeled but prior to the formation of the first phosphodiester bond.
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Affiliation(s)
- Mary C Thomas
- Department of Biochemistry, Case Western Reserve University School of Medicine, Cleveland, OH 44106-4935, USA
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11
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Spresser CR, Carlson KA. Drosophila melanogaster as a complementary system for studying HIV-1-related genes and proteins. J Neurosci Res 2005; 80:451-5. [PMID: 15795932 DOI: 10.1002/jnr.20460] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Human immunodeficiency virus type 1 (HIV-1) persists as a pandemic even though new information about the virus is being discovered on a daily basis. If the brain becomes infected, HIV-1 encephalitis or HIV-1-associated dementia may develop. There is much to be learned about the modes of action and mechanisms of genes and proteins, and their interactions that underlie HIV-1 infection. Drosophila melanogaster has been used successfully to study genes and proteins related to HIV-1 infection, including but not limited to the disturbance of antimicrobial responses by viral protein U and the identification of D. melanogaster analogs to the serine palmitoyltransferase 5 and 6 proteins that play a role in activation of transcription by the HIV-1 Tat protein in human cells. We believe that utilizing D. melanogaster as a complementary system for the study of genes and proteins related to HIV-1 infection will provide useful information that will lead to new studies designed to enhance our understanding of the mechanistic roles of these molecules. In the present study, we focus on the utilization of D. melanogaster as a complementary system for studying HIV-1 related genes and proteins, why this research should be extended, and why this complementary system is an important method for enhancing our understanding of the genetics involved in HIV-1 infection.
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Affiliation(s)
- Cole R Spresser
- Biology Department, University of Nebraska at Kearney, Kearney, Nebraska 68849, USA
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12
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13
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Abstract
Gene transcription can be activated or repressed. Such seemingly simple decisions reflect the coordinated actions of a wide array of proteins. Activators and co-activators work together to stimulate the assembly and activity of the machinery that transcribes the gene, whereas repressors and co-repressors work to achieve the opposite goal. Recent studies show that many proteins often engage in regulatory activities and interactions that cross the activation-repression divide. This article discusses selected examples to illustrate the dynamic nature of the transcriptional regulation process and highlights the important roles of not only the individual proteins but also their communication system.
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Affiliation(s)
- Jun Ma
- Division of Developmental Biology, Cincinnati Children's Hospital Research Foundation, University of Cincinnati College of Medicine, 3333 Burnet Avenue, Cincinnati, OH 45229, USA.
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14
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Chen GY, Muramatsu H, Ichihara-Tanaka K, Muramatsu T. ZEC, a zinc finger protein with novel binding specificity and transcription regulatory activity. Gene 2004; 340:71-81. [PMID: 15556296 DOI: 10.1016/j.gene.2004.06.016] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2003] [Revised: 05/17/2004] [Accepted: 06/03/2004] [Indexed: 10/26/2022]
Abstract
A novel 114-kDa zinc finger protein, ZEC, has been found by cDNA cloning and characterized. ZEC was strongly expressed in the testis, liver and kidney, and also in embryonic stem cells. Epitope-tagged experiments indicated nuclear localization of ZEC. ZEC contained 18 C2H2 zinc fingers which were organized in two clusters. A ZEC binding DNA sequence, C/GA/TA/TGGTTGGTTGC, which we have designated the GT box, was identified by random oligonucleotide binding selection assay. The GT box did not contain binding sites for other previously characterized transcription factors and thus represented a potentially novel DNA target sequence. Electrophoretic mobility shift assay (EMSA) showed that both clusters of zinc fingers bound to the same DNA sequence. Site-directed mutagenesis revealed that the core sequence TTGGTT within the GT box was essential to ZEC binding, while DNA sequences outside of the core sequence enhanced this interaction. Furthermore, co-transfection assays demonstrated that ZEC could activate a reporter luciferase gene driven by this DNA sequence.
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MESH Headings
- Amino Acid Sequence
- Animals
- Base Sequence
- Binding Sites/genetics
- Blotting, Northern
- Blotting, Western
- COS Cells
- Cell Line
- Cell Line, Tumor
- Chlorocebus aethiops
- Cloning, Molecular
- DNA, Complementary/chemistry
- DNA, Complementary/genetics
- DNA-Binding Proteins/genetics
- DNA-Binding Proteins/metabolism
- Electrophoretic Mobility Shift Assay
- Gene Expression Profiling
- Luciferases/genetics
- Luciferases/metabolism
- Male
- Mice
- Mice, Inbred Strains
- Microscopy, Confocal
- Molecular Sequence Data
- Oligonucleotides/genetics
- Oligonucleotides/metabolism
- Protein Binding
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- Recombinant Fusion Proteins/genetics
- Recombinant Fusion Proteins/metabolism
- Sequence Alignment
- Sequence Analysis, DNA
- Sequence Homology, Amino Acid
- Testis/metabolism
- Transcription Factors/genetics
- Transcription Factors/metabolism
- Transfection
- Zinc Fingers/genetics
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Affiliation(s)
- Guo-Yun Chen
- Department of Biochemistry, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa, Nagoya 466-8550, Japan
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15
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Schroeder MD, Pearce M, Fak J, Fan H, Unnerstall U, Emberly E, Rajewsky N, Siggia ED, Gaul U. Transcriptional control in the segmentation gene network of Drosophila. PLoS Biol 2004; 2:E271. [PMID: 15340490 PMCID: PMC514885 DOI: 10.1371/journal.pbio.0020271] [Citation(s) in RCA: 201] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2003] [Accepted: 06/17/2004] [Indexed: 12/21/2022] Open
Abstract
The segmentation gene network of Drosophila consists of maternal and zygotic factors that generate, by transcriptional (cross-) regulation, expression patterns of increasing complexity along the anterior-posterior axis of the embryo. Using known binding site information for maternal and zygotic gap transcription factors, the computer algorithm Ahab recovers known segmentation control elements (modules) with excellent success and predicts many novel modules within the network and genome-wide. We show that novel module predictions are highly enriched in the network and typically clustered proximal to the promoter, not only upstream, but also in intronic space and downstream. When placed upstream of a reporter gene, they consistently drive patterned blastoderm expression, in most cases faithfully producing one or more pattern elements of the endogenous gene. Moreover, we demonstrate for the entire set of known and newly validated modules that Ahab's prediction of binding sites correlates well with the expression patterns produced by the modules, revealing basic rules governing their composition. Specifically, we show that maternal factors consistently act as activators and that gap factors act as repressors, except for the bimodal factor Hunchback. Our data suggest a simple context-dependent rule for its switch from repressive to activating function. Overall, the composition of modules appears well fitted to the spatiotemporal distribution of their positive and negative input factors. Finally, by comparing Ahab predictions with different categories of transcription factor input, we confirm the global regulatory structure of the segmentation gene network, but find odd skipped behaving like a primary pair-rule gene. The study expands our knowledge of the segmentation gene network by increasing the number of experimentally tested modules by 50%. For the first time, the entire set of validated modules is analyzed for binding site composition under a uniform set of criteria, permitting the definition of basic composition rules. The study demonstrates that computational methods are a powerful complement to experimental approaches in the analysis of transcription networks.
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Affiliation(s)
- Mark D Schroeder
- 1Laboratory of Developmental Neurogenetics, Rockefeller UniversityNew York, New York, United States of America
| | - Michael Pearce
- 1Laboratory of Developmental Neurogenetics, Rockefeller UniversityNew York, New York, United States of America
| | - John Fak
- 1Laboratory of Developmental Neurogenetics, Rockefeller UniversityNew York, New York, United States of America
| | - HongQing Fan
- 1Laboratory of Developmental Neurogenetics, Rockefeller UniversityNew York, New York, United States of America
| | - Ulrich Unnerstall
- 1Laboratory of Developmental Neurogenetics, Rockefeller UniversityNew York, New York, United States of America
| | - Eldon Emberly
- 2Center for Studies in Physics and Biology, Rockefeller UniversityNew York, New YorkUnited States of America
| | - Nikolaus Rajewsky
- 2Center for Studies in Physics and Biology, Rockefeller UniversityNew York, New YorkUnited States of America
| | - Eric D Siggia
- 2Center for Studies in Physics and Biology, Rockefeller UniversityNew York, New YorkUnited States of America
| | - Ulrike Gaul
- 1Laboratory of Developmental Neurogenetics, Rockefeller UniversityNew York, New York, United States of America
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16
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Erkine AM. Activation domains of gene-specific transcription factors: are histones among their targets? Biochem Cell Biol 2004; 82:453-9. [PMID: 15284898 DOI: 10.1139/o04-036] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Activation domains of promoter-specific transcription factors are critical entities involved in recruitment of multiple protein complexes to gene promoters. The activation domains often retain functionality when transferred between very diverse eukaryotic phyla, yet the amino acid sequences of activation domains do not bear any specific consensus or secondary structure. Activation domains function in the context of chromatin structure and are critical for chromatin remodeling, which is associated with transcription initiation. The mechanisms of direct and indirect recruitment of chromatin-remodeling and histone-modifying complexes, including mechanisms involving direct interactions between activation domains and histones, are discussed.Key words: activation domain, transcription, chromatin, nucleosome.
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Affiliation(s)
- Alexandre M Erkine
- Division of Basic Biomedical Sciences, University of South Dakota School of Medicine, Vermillion 57069, USA.
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17
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Matyash A, Chung HR, Jäckle H. Genome-wide mapping of in vivo targets of the Drosophila transcription factor Kruppel. J Biol Chem 2004; 279:30689-96. [PMID: 15131112 DOI: 10.1074/jbc.m403345200] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Krüppel (Kr), a member of the gap class of Drosophila segmentation genes, encodes a DNA binding zinc finger-type transcription factor. In addition to its segmentation function at the blastoderm stage, Krüppel also plays a critical role in organ formation during later stages of embryogenesis. To systematically identify in vivo target genes of Krüppel, we isolated DNA fragments from the Krüppel-associated portion of chromatin and used them to find and map Krüppel-dependent cis-acting regulatory sites in the Drosophila genome. We show that Krüppel binding sites are not enriched in Krüppel-associated chromatin and that the clustering of Krüppel binding sites, as found in the cis-acting elements of Krüppel-dependent segmentation genes used for in silico searches of Krüppel target genes, is not a prerequisite for the in vivo binding of Krüppel to its regulatory elements. Results obtained with the newly identified target gene ken and barbie (ken) indicate that Krüppel represses transcription and thereby restricts the spatial expression pattern of ken during blastoderm and gastrulation.
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Affiliation(s)
- Alexey Matyash
- Max-Planck-Institut für biophysikalische Chemie, Abteilung Molekulare Entwicklungsbiologie, D-37070 Göttingen, Germany
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18
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Abstract
In development, cell identity is maintained by epigenetic functions that prevent changes in cell type-specific transcription programs. Recent insights into gene silencing mechanisms by Polycomb group (PcG) and trithorax group (trxG) proteins reveal that the memory system involves a concerted process of chromatin modification, blocking of RNA polymerase II, and synthesis of noncoding RNA. Remarkably, cell memory is regulated by a balance between repressors and activators that maintains both transcription status and at the same time the possibility of switching to a different state.
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Affiliation(s)
- Valerio Orlando
- Dulbecco Telethon Institute, Institute of Genetics & Biophysics CNR, Via Pietro Castellino 111, 80131, Naples, Italy.
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19
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Abstract
Different members of the interferon regulatory factor (IRF) family are early activated by viral infection of eukaryotic cells. The IRFs participate in the virus-induced transcriptional regulation of different genes, including the multigenic interferon-A (IFN-A) family, members of which are involved in the establishment of an antiviral state, cell growth inhibition or apoptosis. This study presents the recent progress in the field of virus-induced transactivation and repression of IFN-A gene promoters. Data presented on the modular organization of IFN-A gene promoters and their transactivation dependent on IRF-3 and IRF-7 provide a new insight on the cooperativity mechanisms among the different IRF family members. Data on the transcriptional repression of virus-induced interferon-A promoters by the homeodomain protein Pitx1 contribute to our understanding of the complex differential transcriptional activation, repression and antirepression of the IFN-A genes.
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Affiliation(s)
- Ahmet Civas
- UPR 2228, CNRS, Laboratoire de régulation transcriptionnelle et maladies génétiques, UFR biomédicale des Saints-Pères, Université Paris V, 45, rue des Saints-Pères, 75270 Paris cedex 6, France.
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20
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Yang Z, Wara-aswapati N, Yoshida Y, Walker N, Galson DL, Listman J, Auron PE. Dual regulatory role of human cytomegalovirus immediate-early protein in IL1B transcription is dependent upon Spi-1/PU.1. Biochem Biophys Res Commun 2002; 294:854-63. [PMID: 12061786 DOI: 10.1016/s0006-291x(02)00562-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Activation of IL1B gene transcription has been shown to play a crucial role in human cytomegalovirus (HCMV) infection. We previously reported that HCMV immediate-early (IE) proteins vigorously transactivate IL1B expression without the need for a normally essential upstream enhancer. This activation appears to depend upon protein-protein tethering between IE2, which provides a transcription activation domain (TAD), and the DNA-binding domain of the transcription factor Spi-1. We now show a distinct mechanism by which IE1 and IE2 mediate both weak Spi-1-independent and vigorous Spi-1-dependent IL1B transcription from the -59 to +12 IL1B core promoter. These results demonstrate that in contrast to non-viral, enhancer-mediated, transactivation of IL1B, the IE mechanism is not absolutely dependent upon Spi-1. However, Spi-1 is required for vigorous transcription. Additionally, we have discovered that IE1, which cooperates with IE2 to transactivate IL1B, has minimal activity in the absence of IE2 and Spi-1. Furthermore, IE1 is a dual-acting factor, which can either activate or repress IL1B, depending on the presence of both IE2 and the Spi-1 TADs. Therefore, the relative expression of IE1 and IE2, which varies during HCMV infection, may provide a molecular mechanism by which IL1B can be repressed, thus, avoiding clearance by the host.
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Affiliation(s)
- Zhiyong Yang
- The New England Baptist Bone and Joint Institute, Beth Israel Deaconess Medical Center, Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
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21
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Pei L. Transcriptional repressor of vasoactive intestinal peptide receptor mediates repression through interactions with TFIIB and TFIIEbeta. Biochem J 2001; 360:633-8. [PMID: 11736653 PMCID: PMC1222266 DOI: 10.1042/0264-6021:3600633] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The transcriptional repressor for rat vasoactive-intestinal-polypeptide receptor 1 (VIPR-RP) is a recently characterized transcription factor that belongs to a family of proteins, which include components of the DNA replication factor C complex. In this study, I investigated the mechanisms by which VIPR-RP represses transcription. I show here that transcriptional repression by VIPR-RP is mediated by a histone deacetylase-independent mechanism. I provide evidence that VIPR-RP makes direct physical contacts with two proteins of the basal transcription apparatus, the transcription factors TFIIB and TFIIEbeta. The interaction with TFIIB is mediated by the N-terminal 180 amino acids, whereas the interactive domain with TFIIEbeta is located between residues 367 and 527 of VIPR-RP. Using gel mobility-shift assays I demonstrated that interaction between VIPR-RP and TFIIB prevents the recruitment of TFIIB into a DNA-TATA-box-binding protein complex. My results indicate that VIPR-RP mediates transcriptional repression through direct interactions with the general transcription machinery.
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Affiliation(s)
- L Pei
- Division of Endocrinology & Metabolism, Cedars-Sinai Research Institute-UCLA School of Medicine, 8700 Beverly Boulevard, Los Angeles, CA 90048, U.S.A.
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22
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Yu X, Li P, Roeder RG, Wang Z. Inhibition of androgen receptor-mediated transcription by amino-terminal enhancer of split. Mol Cell Biol 2001; 21:4614-25. [PMID: 11416139 PMCID: PMC87125 DOI: 10.1128/mcb.21.14.4614-4625.2001] [Citation(s) in RCA: 82] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A yeast two-hybrid assay has identified an androgen-dependent interaction of androgen receptor (AR) with amino-terminal enhancer of split (AES), a member of the highly conserved Groucho/TLE family of corepressors. Full-length AR, as well as the N-terminal fragment of AR, showed direct interactions with AES in in vitro protein-protein interaction assays. AES specifically inhibited AR-mediated transcription in a well-defined cell-free transcription system and interacted specifically with the basal transcription factor (TFIIE) in HeLa nuclear extract. These observations implicate AES as a selective repressor of ligand-dependent AR-mediated transcription that acts by directly interacting with AR and by targeting the basal transcription machinery.
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Affiliation(s)
- X Yu
- Laboratory of Biochemistry and Molecular Biology, The Rockefeller University, New York, New York 10021, USA
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23
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Faitar SL, Brodie SA, Ponticelli AS. Promoter-specific shifts in transcription initiation conferred by yeast TFIIB mutations are determined by the sequence in the immediate vicinity of the start sites. Mol Cell Biol 2001; 21:4427-40. [PMID: 11416123 PMCID: PMC87103 DOI: 10.1128/mcb.21.14.4427-4440.2001] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The general transcription factor IIB (TFIIB) is required for transcription of class II genes by RNA polymerase II. Previous studies demonstrated that mutations in the Saccharomyces cerevisiae SUA7 gene, which encodes TFIIB, can alter transcription initiation patterns in vivo. To further delineate the functional domain and residues of TFIIB involved in transcription start site utilization, a genetic selection was used to isolate S. cerevisiae TFIIB mutants exhibiting downstream shifts in transcription initiation in vivo. Both dominant and recessive mutations conferring downstream shifts were identified at multiple positions within a highly conserved homology block in the N-terminal region of the protein. The TFIIB mutations conferred downstream shifts in transcription initiation at the ADH1 and CYC1 promoters, whereas no significant shifts were observed at the HIS3 promoter. Analysis of a series of ADH1-HIS3 hybrid promoters and variant ADH1 and HIS3 promoters containing insertions, deletions, or site-directed base substitutions revealed that the feature that renders a promoter sensitive to TFIIB mutations is the sequence in the immediate vicinity of the normal start sites. We discuss these results in light of possible models for the mechanism of start site utilization by S. cerevisiae RNA polymerase II and the role played by TFIIB.
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Affiliation(s)
- S L Faitar
- Department of Biochemistry and the Center for Advanced Molecular Biology and Immunology, School of Medicine and Biomedical Sciences, State University of New York at Buffalo, Buffalo, New York 14214-3000, USA
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24
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Ren Y, Liao WS. Transcription factor AP-2 functions as a repressor that contributes to the liver-specific expression of serum amyloid A1 gene. J Biol Chem 2001; 276:17770-8. [PMID: 11278660 DOI: 10.1074/jbc.m010307200] [Citation(s) in RCA: 23] [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
We previously identified transcription factor AP-2 as the nuclear factor that interacts with the tissue-specific repressor element in the rat serum amyloid A1 (SAA1) promoter. In this report, we provide evidence for a second AP-2-binding site and show that both AP-2 sites participate in mediating the transcription repression of SAA1 promoter. This proximal AP-2 site overlaps with the NFkappaB-binding site known to be essential for SAA1 promoter activity. Protein binding competition experiments demonstrated that AP-2 and NFkappaB binding to these overlapping sites were mutually exclusive. Furthermore, the addition of AP-2 easily displaced prebound NFkappaB, whereas NFkappaB could not displace AP-2. These results thus suggest that one mechanism by which AP-2 negatively regulates SAA1 promoter activity may be by antagonizing the function of NFkappaB. Consistent with a repression function, transient expression of AP-2 in HepG2 cells inhibited conditioned medium-induced SAA1 promoter activation. This inhibition was dependent on functional AP-2-binding sites, since mutation of AP-2-binding sites abolished inhibitory effects of AP-2 in HepG2 cells as well as resulted in derepression of the SAA1 promoter in HeLa cells. In addition to SAA1, we found that several other liver gene promoters also contain putative AP-2-binding sites. Some of these sequences could specifically inhibit AP-2.DNA complex formation, and for the human complement C3 promoter, overexpression of AP-2 also could repress its cytokine-mediated activation. Finally, stable expression of AP-2 in hepatoma cells significantly reduced the expression of endogenous SAA, albumin, and alpha-fetoprotein genes. Taken together, our results suggest that AP-2 may function as a transcription repressor to inhibit the expression of not only SAA1 gene but also other liver genes in nonhepatic cells.
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Affiliation(s)
- Y Ren
- Department of Biochemistry and Molecular Biology, Program in Genes and Development, The University of Texas M. D. Anderson Cancer Center, Houston, Texas 77030, USA
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25
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Garriga-Canut M, Roopra A, Buckley NJ. The basic helix-loop-helix protein, sharp-1, represses transcription by a histone deacetylase-dependent and histone deacetylase-independent mechanism. J Biol Chem 2001; 276:14821-8. [PMID: 11278948 DOI: 10.1074/jbc.m011619200] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Many aspects of neurogenesis and neuronal differentiation are controlled by basic helix-loop-helix (bHLH) proteins. One such factor is SHARP-1, initially identified on the basis of its sequence similarity to hairy. Unlike hairy, and atypically for bHLHs, SHARP-1 is expressed late in development, suggestive of a role in terminal aspects of differentiation. Nevertheless, the role of SHARP-1 and the identity of its target genes remain unknown. During the course of a one-hybrid screen for transcription factors that bind to regulatory domains of the M1 muscarinic acetylcholine receptor gene, we isolated the bHLH transcription factor SHARP-1. In this study, we investigated the functional role of SHARP-1 in regulating transcription. Fusion proteins of SHARP-1 tethered to the gal4 DNA binding domain repress both basal and activated transcription when recruited to either a TATA-containing or a TATAless promoter. Furthermore, we identified two independent repression domains that operate via distinct mechanisms. Repression by a domain in the C terminus is sensitive to the histone deacetylase inhibitor trichostatin A, whereas repression by the bHLH domain is insensitive to TSA. Furthermore, overexpression of SHARP-1 represses transcription from the M(1) promoter. This study represents the first report to assign a function to, and to identify a target gene for, the bHLH transcription factor SHARP-1.
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Affiliation(s)
- M Garriga-Canut
- Schools of Biochemistry and Molecular Biology and Biomedical Sciences, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, United Kingdom
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26
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Browning CM, Smith MJ, Clark NM, Lane BR, Parada C, Montano M, KewalRamani VN, Littman DR, Essex M, Roeder RG, Markovitz DM. Human GLI-2 is a tat activation response element-independent Tat cofactor. J Virol 2001; 75:2314-23. [PMID: 11160734 PMCID: PMC114814 DOI: 10.1128/jvi.75.5.2314-2323.2001] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2000] [Accepted: 12/07/2000] [Indexed: 11/20/2022] Open
Abstract
Zinc finger-containing GLI proteins are involved in the development of Caenorhabditis elegans, Xenopus, Drosophila, zebrafish, mice, and humans. In this study, we show that an isoform of human GLI-2 strongly synergizes with the Tat transactivating proteins of human immunodeficiency virus types 1 and 2 (HIV-1 and -2) and markedly stimulates viral replication. GLI-2 also synergizes with the previously described Tat cofactor cyclin T1 to stimulate Tat function. Surprisingly, GLI-2/Tat synergy is not dependent on either a typical GLI DNA binding site or an intact Tat activation response element but does require an intact TATA box. Thus, GLI-2/Tat synergy results from a mechanism of action which is novel both for a GLI protein and for a Tat cofactor. These findings link the GLI family of transcriptional and developmental regulatory proteins to Tat function and HIV replication.
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Affiliation(s)
- C M Browning
- Department of Microbiology and Immunology, Ann Arbor, Michigan 48109-0640,USA
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27
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Guiral M, Bess K, Goodwin G, Jayaraman PS. PRH represses transcription in hematopoietic cells by at least two independent mechanisms. J Biol Chem 2001; 276:2961-70. [PMID: 11054411 DOI: 10.1074/jbc.m004948200] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
PRH (proline-rich homeodomain protein) is strongly expressed in the hematopoietic compartment. Here we show that PRH is a repressor of transcription in hematopoietic cells. A fragment of PRH that includes the homeodomain can bind to TATA box sequences in vitro and can also bind to the TATA box-binding protein. PRH represses transcription from TATA box-containing promoters in intact cells but does not repress transcription from a promoter lacking a TATA box. A mutation in the PRH homeodomain that blocks binding to DNA but that has little or no effect on binding to the TATA box-binding protein significantly reduces the ability of the protein to repress transcription and provides the first clear demonstration that a homeodomain can bring about transcriptional repression in vivo by binding to a TATA box. However, we also show that mutation of the PRH homeodomain does not block the ability of PRH to repress transcription when this protein is tethered upstream of the TATA box via a heterologous DNA-binding domain. PRH also contains an N-terminal proline-rich repression domain that is separate from the homeodomain. Deletion mapping suggests that this repression domain contains at least two regions that both independently contribute to transcriptional repression.
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Affiliation(s)
- M Guiral
- Department of Biochemistry, University of Bristol, University Walk, Bristol, United Kingdom
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28
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Xaus J, Comalada M, Barrachina M, Herrero C, Goñalons E, Soler C, Lloberas J, Celada A. The expression of MHC class II genes in macrophages is cell cycle dependent. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2000; 165:6364-71. [PMID: 11086074 DOI: 10.4049/jimmunol.165.11.6364] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Using different drugs, we stopped the cell cycle of bone marrow-derived macrophages at different points. After IFN-gamma stimulation, macrophages arrested at the G(1) phase of the cell cycle did not increase cell surface expression of the MHC class II IA. This inhibition is specific, because, under the same conditions, IFN-gamma induces the expression of Fcgamma receptors and the inducible NO synthase mRNA. Treatments that inhibit macrophage proliferation by blocking the cell cycle at the G(1) phase, such as adenosine, forskolin, or LPS, blocked the IFN-gamma induction of IA. Under IFN-gamma treatment, the steady-state levels of IAalpha and IAss mRNA did not increase in cells arrested at the G(1) phase and the half-life of the MHC mRNA was not modified. These data suggest that the cell cycle modulation of IFN-gamma-induced MHC II gene expression occurs at the transcriptional level. The expression of the class II transactivator mRNA induced by IFN-gamma was also blocked when macrophages were arrested at the G(1) phase of the cell cycle, suggesting that the lack of IFN-gamma response occurs at the early steps of MHC class II expression. Finally, macrophages arrested at the G(1) phase showed increased basal levels of cell surface IA due to an increase of the translational efficiency. These data show that the expression of MHC class II genes is regulated by the cell cycle.
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Affiliation(s)
- J Xaus
- Departament de Fisiologia (Biologia del Macròfag), Facultat de Biologia and Fundació August Pi i Sunyer, Campus de Bellvitge, Universitat de Barcelona, Barcelona, Spain
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29
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Perrone L, Pasca di Magliano M, Zannini M, Di Lauro R. The thyroid transcription factor 2 (TTF-2) is a promoter-specific DNA-binding independent transcriptional repressor. Biochem Biophys Res Commun 2000; 275:203-8. [PMID: 10944465 DOI: 10.1006/bbrc.2000.3232] [Citation(s) in RCA: 44] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The thyroid transcription factor TTF-2 is a forkhead-containing protein involved in thyroid-specific gene expression and necessary for thyroid morphogenesis. In this paper, we demonstrate that TTF-2 is able to inhibit the activity of the thyroid-specific transcription factors TTF-1 and Pax-8 only on certain promoters. We identified the minimal protein domain responsible for repressor activity, which behaves as an independent functional domain, and we show that repression by TTF-2 is DNA-binding independent. We suggest that TTF-2 is able to interfere with a specific cofactor required for TTF-1 and Pax-8 activity.
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Affiliation(s)
- L Perrone
- Stazione Zoologica "Anton Dohrn,", Naples, 80121, Italy
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30
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Peng H, Begg GE, Harper SL, Friedman JR, Speicher DW, Rauscher FJ. Biochemical analysis of the Kruppel-associated box (KRAB) transcriptional repression domain. J Biol Chem 2000; 275:18000-10. [PMID: 10748030 DOI: 10.1074/jbc.m001499200] [Citation(s) in RCA: 89] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The Kruppel-associated box (KRAB) domain is a 75-amino acid transcriptional repressor module commonly found in eukaryotic zinc finger proteins. KRAB-mediated gene silencing requires binding to the RING-B box-coiled-coil domain of the corepressor KAP-1. Little is known about the biochemical properties of the KRAB domain or the KRAB.KAP-1 complex. Using purified components, a combination of biochemical and biophysical analyses has revealed that the KRAB domain from the KOX1 protein is predominantly a monomer and that the KAP-1 protein is predominantly a trimer in solution. The analyses of electrophoretic mobility shift assays, GST association assays, and plasmon resonance interaction data have indicated that the KRAB binding to KAP-1 is direct, highly specific, and high affinity. The optical biosensor data for the complex was fitted to a model of a one-binding step interaction with fast association and slow dissociation rates, with a calculated K(d) of 142 nm. The fitted R(max) indicated three molecules of KAP-1 binding to one molecule of the KRAB domain, a stoichiometry that is consistent with quantitative SDS-polyacrylamide gel electrophoresis analysis of the complex. These structural and dynamic parameters of the KRAB/KAP-1 interaction have implications for identifying downstream effectors of KAP-1 silencing and the de novo design of new repression domains.
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Affiliation(s)
- H Peng
- Wistar Institute, Philadelphia, Pennsylvania 19104, USA
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31
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Huang CF, Wang YC, Tsao DA, Tung SF, Lin YS, Wu CW. Antagonism between members of the CNC-bZIP family and the immediate-early protein IE2 of human cytomegalovirus. J Biol Chem 2000; 275:12313-20. [PMID: 10766871 DOI: 10.1074/jbc.275.16.12313] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
The HCMV IE2 protein negatively autoregulates its own expression as well as represses the transactivation activity of p53. Using the repression domain of IE2 as bait in the yeast two-hybrid system, Nrf1 and Nrf2, members of the CNC-bZIP family, were found to be IE2-interacting proteins. Residues 331-448 encompassing the DNA-binding and the dimerization domains of Nrf1 are sufficient for the interaction. The interaction was further confirmed in vitro by a glutathione S-transferase pull-down assay and in vivo by co-immunoprecipitation. In transient transfection studies, transcription driven by six copies of an NF-E2 site or by chimeric proteins between the DNA-binding domain of LexA and members of the CNC-bZIP family is repressed by IE2. Importantly, the DNA binding activity of the Nrf1/MafK heterodimer is not impeded by IE2. In a parallel study, CNC-bZIP factors attenuate the negative autoregulation of IE2. The attenuation could be explained by the finding that Nrf1 functions alone and synergistically with its heterodimerization partner, MafK, in inhibiting the DNA binding activity of IE2. Taken together, these results demonstrate the existence of antagonism between members of the CNC-bZIP family and IE2.
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Affiliation(s)
- C F Huang
- Institute of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan
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32
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Kang SW, Kuzuhara T, Horikoshi M. Functional interaction of general transcription initiation factor TFIIE with general chromatin factor SPT16/CDC68. Genes Cells 2000; 5:251-63. [PMID: 10792464 DOI: 10.1046/j.1365-2443.2000.00323.x] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
BACKGROUND Transcriptional initiation of class II genes is one of the major targets for the regulation of gene expression and is carried out by RNA polymerase II and many auxiliary factors, which include general transcription initiation factors (GTFs). TFIIE, one of the GTFs, functions at the later stage of transcription initiation. As recent studies indicated the possibility that TFIIE may have a role in chromatin transcriptional regulation, we isolated TFIIE-interacting factors which have chromatin-related functions. RESULTS Using the yeast two-hybrid screening system, we isolated the C-terminal part of the human homologue of Saccharomyces cerevisiae (y) Spt16p/Cdc68p, a general chromatin factor. The C-terminal part of human SPT16/CDC68 directly interacts with TFIIE, and ySpt16p/Cdc68p also interacts with yTFIIE (Tfa1p/Tfa2p), thus indicating the existence of an evolutionarily conserved interaction between TFIIE and SPT16/CDC68. Functional interaction of yTFIIE and ySpt16p/Cdc68p was examined using a conditional yTFIIE-alpha mutant strain. Over-expression of ySpt16p/Cdc68p suppressed the phenotype of cold sensitivity of the yTFIIE-alpha-cs mutant strain, and in vitro binding assays revealed that yTFIIE-alpha-cs mutant protein showed diminished binding affinity to ySpt16p/Cdc68p. CONCLUSIONS These observations indicate that general transcription initiation factor TFIIE functionally interacts with general chromatin factor SPT16/CDC68, a finding which provides new insight into the involvement of TFIIE in chromatin transcription. This may well lead to a breakthrough in relationships between the transcription initiation process and structural changes in chromatin.
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Affiliation(s)
- S W Kang
- Laboratory of Developmental Biology, Institute of Molecular and Cellular Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
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33
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Shimell MJ, Peterson AJ, Burr J, Simon JA, O'Connor MB. Functional analysis of repressor binding sites in the iab-2 regulatory region of the abdominal-A homeotic gene. Dev Biol 2000; 218:38-52. [PMID: 10644409 DOI: 10.1006/dbio.1999.9576] [Citation(s) in RCA: 82] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Spatial boundaries of homeotic gene expression are initiated and maintained by two sets of transcriptional repressors: the gap gene products and the Polycomb group proteins. Previously, the Hunchback (HB) protein has been implicated in setting the anterior expression limit of the UBX homeotic protein in parasegment 6. Here we investigate DNA elements and trans-acting repressors that control spatial expression of the Abdominal-A (ABD-A) homeotic protein. Analysis of a 1.7-kb enhancer element [iab-2(1.7)] from the iab-2 regulatory region shows that in contrast to Ubx enhancer elements, both HB and Krüppel (KR) are required to set the ABD-A anterior boundary in parasegment 7. DNase I footprinting and site-directed mutagenesis show that HB and KR are direct regulators of this iab-2 enhancer. The single KR site can be moved to a new location 100 bp away and still maintain repressive activity, whereas relocation by 300 bp abolishes activity. These results suggest that KR repression occurs through a local quenching mechanism. We also show that the gap repressor Giant (GT) initially establishes a posterior expression limit at PS9, which shifts posteriorly after the blastoderm stage. Finally, we show that this iab-2 enhancer contains multiple binding sites for the Polycomb group protein Pleiohomeotic (PHO). These iab-2 PHO sites are required in vivo for chromosome pairing-dependent repression of a mini-white reporter. However, the PHO sites are not sufficient to maintain repression of a homeotic reporter gene anterior to PS7. Full maintenance at late embryonic stages requires additional sequences adjacent to the iab-2(1.7) enhancer.
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Affiliation(s)
- M J Shimell
- Department of Genetics, University of Minnesota, Minneapolis, Minnesota, 55455, USA
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34
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Glass CK, Rosenfeld MG. The coregulator exchange in transcriptional functions of nuclear receptors. Genes Dev 2000. [DOI: 10.1101/gad.14.2.121] [Citation(s) in RCA: 900] [Impact Index Per Article: 37.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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35
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La Rosée-Borggreve A, Häder T, Wainwright D, Sauer F, Jäckle H. hairy stripe 7 element mediates activation and repression in response to different domains and levels of Krüppel in the Drosophila embryo. Mech Dev 1999; 89:133-40. [PMID: 10559488 DOI: 10.1016/s0925-4773(99)00219-1] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
The Drosophila gap gene Krüppel (Kr) encodes a zinc finger-type transcription factor required for controlling the spatial expression of other segmentation genes during early blastoderm stage. Here we show that two independent and transferable repressor domains of Krüppel act to control expression of the pair-rule gene hairy, and that the minimal cis-acting element of hairy stripe7 (h7) mediates either Krüppel-dependent activation or repression in different regions of the blastoderm embryo. The C-terminal region of Krüppel which encompasses the predominant repressor domain is not essential for activation, but is required to fully suppress h7-mediated transcription in response to high levels of Krüppel activity. This domain contains an interaction motif for dCtBP, a homologue of the human co-repressor CtBP. dCtBP activity is, however, dispensable for Krüppel-mediated repression in the embryo since Krüppel-mediated repression functions in the absence of dCtBP. Possible modes of h7-mediated gene regulation in response to the different domains and levels of Krüppel are discussed.
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Affiliation(s)
- A La Rosée-Borggreve
- Abteilung Molekulare Entwicklungsbiologie, Max-Planck-Institut für biophysikalische Chemie, Am Fassberg, D-37077, Göttingen, Germany
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36
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Abstract
Erythroid Kruppel like factor (EKLF) is the founding member of a family of transcription factors which are defined by the presence of three C-terminal C2H2-type zinc fingers. Since its discovery 6 years ago, the study of EKLF has been intense. In this review I will revisit the discovery of EKLF, and highlight recent advances in our understanding of how it interacts with other proteins to regulate erythroid gene transcription. The current knowledge of the biological role/s of EKLF in erythroid cell differentiation and globin gene switching are summarized.
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Affiliation(s)
- A Perkins
- Department of Physiology, Monash University, Clayton, Victoria, Australia
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37
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Bangur CS, Faitar SL, Folster JP, Ponticelli AS. An interaction between the N-terminal region and the core domain of yeast TFIIB promotes the formation of TATA-binding protein-TFIIB-DNA complexes. J Biol Chem 1999; 274:23203-9. [PMID: 10438492 DOI: 10.1074/jbc.274.33.23203] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The general transcription factor IIB (TFIIB) plays an essential role in transcription of protein-coding genes by eukaryotic RNA polymerase II. We previously identified a yeast TFIIB mutant (R64E) that exhibited increased activity in the formation of stable TATA-binding protein-TFIIB-DNA (DB) complexes in vitro. We report here that the homologous human TFIIB mutant (R53E) also displayed increased activity in DB complex formation in vitro. Biochemical analyses revealed that the increased activity of the R64E mutant in DB complex formation was associated with an altered protease sensitivity of the protein and an enhanced interaction between the N-terminal region and the C-terminal core domain. These results suggest that the intramolecular interaction in yeast TFIIB stabilizes a productive conformation of the protein for the association with promoter-bound TATA-binding protein.
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Affiliation(s)
- C S Bangur
- Department of Biochemistry and the Center for Advanced Molecular Biology and Immunology, School of Medicine and Biomedical Sciences, State University of New York, Buffalo, New York 14214-3000, USA
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38
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Ryan RF, Schultz DC, Ayyanathan K, Singh PB, Friedman JR, Fredericks WJ, Rauscher FJ. KAP-1 corepressor protein interacts and colocalizes with heterochromatic and euchromatic HP1 proteins: a potential role for Krüppel-associated box-zinc finger proteins in heterochromatin-mediated gene silencing. Mol Cell Biol 1999; 19:4366-78. [PMID: 10330177 PMCID: PMC104396 DOI: 10.1128/mcb.19.6.4366] [Citation(s) in RCA: 310] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Krüppel-associated box (KRAB) domains are present in approximately one-third of all human zinc finger proteins (ZFPs) and are potent transcriptional repression modules. We have previously cloned a corepressor for the KRAB domain, KAP-1, which is required for KRAB-mediated repression in vivo. To characterize the repression mechanism utilized by KAP-1, we have analyzed the ability of KAP-1 to interact with murine (M31 and M32) and human (HP1alpha and HP1gamma) homologues of the HP1 protein family, a class of nonhistone heterochromatin-associated proteins with a well-established epigenetic gene silencing function in Drosophila. In vitro studies confirmed that KAP-1 is capable of directly interacting with M31 and hHP1alpha, which are normally found in centromeric heterochromatin, as well as M32 and hHP1gamma, both of which are found in euchromatin. Mapping of the region in KAP-1 required for HP1 interaction showed that amino acid substitutions which abolish HP1 binding in vitro reduce KAP-1 mediated repression in vivo. We observed colocalization of KAP-1 with M31 and M32 in interphase nuclei, lending support to the biochemical evidence that M31 and M32 directly interact with KAP-1. The colocalization of KAP-1 with M31 is sometimes found in subnuclear territories of potential pericentromeric heterochromatin, whereas colocalization of KAP-1 and M32 occurs in punctate euchromatic domains throughout the nucleus. This work suggests a mechanism for the recruitment of HP1-like gene products by the KRAB-ZFP-KAP-1 complex to specific loci within the genome through formation of heterochromatin-like complexes that silence gene activity. We speculate that gene-specific repression may be a consequence of the formation of such complexes, ultimately leading to silenced genes in newly formed heterochromatic chromosomal environments.
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Affiliation(s)
- R F Ryan
- The Wistar Institute, Philadelphia, Pennsylvania, USA
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39
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Shushan EB, Cerasi E, Melloul D. Regulation of the insulin gene by glucose: stimulation of trans-activation potency of human PDX-1 N-terminal domain. DNA Cell Biol 1999; 18:471-9. [PMID: 10390156 DOI: 10.1089/104454999315196] [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: 11/12/2022] Open
Abstract
The beta cells in pancreatic islets of Langerhans increase insulin gene transcription in response to glucose. The pancreatic and duodenal homeobox-1 (PDX-1) plays a major role in glucose-induced insulin transcription. We studied the functional regions of the human PDX-1 protein fused to the DNA-binding domain of the transcription factor Gal4. The results indicate that the N-terminal domain of the hPDX-1, required for transactivation (amino acids 1-120) in transfected betaTC6 and HeLa cells, is also regulated by extracellular glucose concentrations in transfected rat islets. Deletion analyses have led to the mapping of two regions within the N terminus that are essential for its trans-activation properties. One sequence spans amino acids 97-120 in transfected islet and HeLa cells or amino acids 77-120 in betaTC6 cells; the other includes the highly conserved B box (amino acids 31-41). We thus present evidence of a glucose effect on hPDX-1 trans-activation activity, in addition to the previously described regulatory effect on its DNA-binding activity.
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Affiliation(s)
- E B Shushan
- Department of Endocrinology & Metabolism, Hebrew University, Hadassah Medical Center, Jerusalem, Israel
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40
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He GP, Kim S, Ro HS. Cloning and characterization of a novel zinc finger transcriptional repressor. A direct role of the zinc finger motif in repression. J Biol Chem 1999; 274:14678-84. [PMID: 10329662 DOI: 10.1074/jbc.274.21.14678] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
We have identified a novel transcriptional repressor, AEBP2, that binds to a regulatory sequence (termed AE-1) located in the proximal promoter region of the aP2 gene that encodes the adipose fatty acid-binding protein. Sequence analysis of AEBP2 cDNA revealed that it encodes a protein containing three Gli-Krüppel (Cys2-His2)-type zinc fingers. Northern blot analysis revealed two transcripts (4.5 and 3.5 kilobases) which were ubiquitously expressed in every mouse tissue examined. In co-transfection assays, AEBP2 repressed transcription from the homologous aP2 promoter containing multiple copies of the AE-1 sequence. Moreover, a chimeric construct encoding a fusion AEBP2 protein with the Gal4 DNA-binding domain was able to repress the transcriptional activity of a heterologous promoter containing the Gal4-binding sequence. The transcriptional repression function of AEBP2 was completely abolished when one of the conserved histidine residues and a flanking serine residue in the middle zinc finger were replaced with an arginine residue. The defective transcriptional repression function of the mutant derivative was due neither to lack of expression nor to a failure to localize to the nucleus. Moreover, both the wild-type and mutant derivative of either the histidine-tagged recombinant AEBP2 proteins or the in vitro translated Gal4-AEBP2 fusion proteins were equally able to bind to the target DNA. These results suggest that a portion of the zinc finger structure may play a direct role in transcriptional repression function, but not in DNA binding.
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Affiliation(s)
- G P He
- Department of Biochemistry, Faculty of Medicine, Sir Charles Tupper Medical Building, Dalhousie University, Halifax, Nova Scotia B3H 4H7, Canada
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41
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Martin ME, Berk AJ. Corepressor required for adenovirus E1B 55,000-molecular-weight protein repression of basal transcription. Mol Cell Biol 1999; 19:3403-14. [PMID: 10207064 PMCID: PMC84133 DOI: 10.1128/mcb.19.5.3403] [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: 11/20/2022] Open
Abstract
Adenovirus E1B 55,000-molecular-weight protein (55K) binds to host cell p53, stabilizing it, greatly increasing its affinity for its cognate DNA-binding site, and converting it from a regulated activator to a constitutive repressor. Here we analyzed the mechanism of repression by the p53-E1B 55K complex. E1B 55K repression requires that 55K be tethered to the promoter by binding directly to DNA-bound p53. Transcription from an assembled, p53-activated preinitiation complex was not repressed by the subsequent addition of E1B 55K, suggesting that either sites of 55K interaction with p53 or targets of 55K in the preinitiation complex are blocked. Specific E1B 55K repression was observed in reactions lacking TFIIA and with recombinant TATA-binding protein in place of TFIID, conditions under which p53 does not activate transcription. Thus, E1B 55K does not simply inhibit a p53-specific activation mechanism but rather blocks basal transcription. As a consequence, E1B 55K may repress transcription from any promoter with an associated p53-binding site, no matter what other activators associate with the promoter. E1B 55K did not repress basal transcription in reactions with recombinant and highly purified general transcription factors and RNA polymerase II but rather required a corepressor that copurifies with the polymerase.
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Affiliation(s)
- M E Martin
- Molecular Biology Institute and Department of Microbiology and Molecular Genetics, University of California, Los Angeles, Los Angeles, California 90095-1570, USA
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42
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Abstract
Small differences in the levels of an extracellular signaling molecule can specify cell fate during development. Threshold responses are often determined at the level of transcription. Cell-specific and spatially localized patterns of gene expression depend on combinations of sequence-specific activators and repressors that bind to extensive cis-regulatory regions. Different mechanisms for integrating this complex regulatory information are discussed, particularly the role of coregulatory proteins, which are recruited to the DNA template by sequence-specific transcription factors. Recent studies suggest that a growing set of coactivators and corepressors mediate communication between diverse upstream regulatory proteins and the core RNA polymerase II transcription complex.
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Affiliation(s)
- M Mannervik
- Department of Molecular and Cell Biology, 401 Barker Hall, University of California, Berkeley, CA 94720, USA
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43
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Ghosh AK, Steele R, Ray RB. Functional domains of c-myc promoter binding protein 1 involved in transcriptional repression and cell growth regulation. Mol Cell Biol 1999; 19:2880-6. [PMID: 10082554 PMCID: PMC84081 DOI: 10.1128/mcb.19.4.2880] [Citation(s) in RCA: 46] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We initially identified c-myc promoter binding protein 1 (MBP-1), which negatively regulates c-myc promoter activity, from a human cervical carcinoma cell expression library. Subsequent studies on the biological role of MBP-1 demonstrated induction of cell death in fibroblasts and loss of anchorage-independent growth, reduced invasive ability, and tumorigenicity of human breast carcinoma cells. To investigate the potential role of MBP-1 as a transcriptional regulator, a chimeric protein containing MBP-1 fused to the DNA binding domain of the yeast transactivator factor GAL4 was constructed. This fusion protein exhibited repressor activity on the herpes simplex virus thymidine kinase promoter via upstream GAL4 DNA binding sites. Structure-function analysis of mutant MBP-1 in the context of the GAL4 DNA binding domain revealed that MBP-1 transcriptional repressor domains are located in the N terminus (amino acids 1 to 47) and C terminus (amino acids 232 to 338), whereas the activation domain lies in the middle (amino acids 140 to 244). The N-terminal domain exhibited stronger transcriptional repressor activity than the C-terminal region. When the N-terminal repressor domain was transferred to a potent activator, transcription was strongly inhibited. Both of the repressor domains contained hydrophobic regions and had an LXVXL motif in common. Site-directed mutagenesis in the repressor domains indicated that the leucine residues in the LXVXL motif are required for transcriptional repression. Mutation of the leucine residues in the common motif of MBP-1 also abrogated the repressor activity on the c-myc promoter. In addition, the leucine mutant forms of MBP-1 failed to suppress cell growth in fibroblasts like wild-type MBP-1. Taken together, our results indicate that MBP-1 is a complex cellular factor containing multiple transcriptional regulatory domains that play an important role in cell growth regulation.
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Affiliation(s)
- A K Ghosh
- Department of Pathology, Saint Louis University, St. Louis, Missouri 63104, USA
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44
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Jiménez G, Verrijzer CP, Ish-Horowicz D. A conserved motif in goosecoid mediates groucho-dependent repression in Drosophila embryos. Mol Cell Biol 1999; 19:2080-7. [PMID: 10022895 PMCID: PMC84001 DOI: 10.1128/mcb.19.3.2080] [Citation(s) in RCA: 57] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/1998] [Accepted: 12/03/1998] [Indexed: 11/20/2022] Open
Abstract
Surprisingly small peptide motifs can confer critical biological functions. One example is the WRPW tetrapeptide present in the Hairy family of transcriptional repressors, which mediates recruitment of the Groucho (Gro) corepressor to target promoters. We recently showed that Engrailed (En) is another repressor that requires association with Gro for its function. En lacks a WRPW motif; instead, it contains another short conserved sequence, the En homology region 1 (eh1)/GEH motif, that is likely to play a role in tethering Gro to the promoter. Here, we characterize a repressor domain from the Goosecoid (Gsc) developmental regulator that includes an eh1/GEH-like motif. We demonstrate that this domain (GscR) mediates efficient repression in Drosophila blastoderm embryos and that repression by GscR requires Gro function. GscR and Gro interact in vitro, and the eh1/GEH motif is necessary and sufficient for the interaction and for in vivo repression. Because WRPW- and eh1/GEH-like motifs are present in different proteins and in many organisms, the results suggest that interactions between short peptides and Gro represent a widespread mechanism of repression. Finally, we investigate whether Gro is part of a stable multiprotein complex in the nucleus. Our results indicate that Gro does not form stable associations with other proteins but that it may be able to assemble into homomultimeric complexes.
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Affiliation(s)
- G Jiménez
- Developmental Genetics, Imperial Cancer Research Fund, London WC2A 3PX, England, UK.
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45
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Nibu Y, Zhang H, Bajor E, Barolo S, Small S, Levine M. dCtBP mediates transcriptional repression by Knirps, Krüppel and Snail in the Drosophila embryo. EMBO J 1998; 17:7009-20. [PMID: 9843507 PMCID: PMC1171049 DOI: 10.1093/emboj/17.23.7009] [Citation(s) in RCA: 168] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The pre-cellular Drosophila embryo contains 10 well characterized sequence-specific transcriptional repressors, which represent a broad spectrum of DNA-binding proteins. Previous studies have shown that two of the repressors, Hairy and Dorsal, recruit a common co-repressor protein, Groucho. Here we present evidence that three different repressors, Knirps, Krüppel and Snail, recruit a different co-repressor, dCtBP. Mutant embryos containing diminished levels of maternal dCtBP products exhibit both segmentation and dorsoventral patterning defects, which can be attributed to loss of Krüppel, Knirps and Snail activity. In contrast, the Dorsal and Hairy repressors retain at least some activity in dCtBP mutant embryos. dCtBP interacts with Krüppel, Knirps and Snail through a related sequence motif, PXDLSXK/H. This motif is essential for the repression activity of these proteins in transgenic embryos. We propose that dCtBP represents a major form of transcriptional repression in development, and that the Groucho and dCtBP co-repressors mediate separate pathways of repression.
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Affiliation(s)
- Y Nibu
- Department of Molecular and Cellular Biology, Division of Genetics, 401 Barker Hall, University of California, Berkeley, CA 94720, USA
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46
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Gebelein B, Fernandez-Zapico M, Imoto M, Urrutia R. KRAB-independent suppression of neoplastic cell growth by the novel zinc finger transcription factor KS1. J Clin Invest 1998; 102:1911-9. [PMID: 9835615 PMCID: PMC509142 DOI: 10.1172/jci1919] [Citation(s) in RCA: 42] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
The study of zinc finger proteins has revealed their potential to act as oncogenes or tumor suppressors. Here we report the molecular, biochemical, and functional characterization of KS1 (KRAB/zinc finger suppressor protein 1), a novel, ubiquitously expressed zinc finger gene initially isolated from a rat pancreas library. KS1 contains 10 C2H2 zinc fingers, a KRAB-A/B motif, and an ID sequence that has been shown previously to participate in growth factor-regulated gene expression. Northern blot analysis using pancreatic cell lines demonstrates that KS1 mRNA is inducible by serum and epidermal growth factor, suggesting a role for this gene in cell growth regulation. Biochemical analysis reveals that KS1 is a nuclear protein containing two transcriptional repressor domains, R1 and R2. R1 corresponds to the KRAB-A motif, whereas R2 represents a novel sequence. Transformation assays using NIH3T3 cells demonstrate that KS1 suppresses transformation by the potent oncogenes Ha-ras, Galpha12, and Galpha13. Deletion of the R1/ KRAB-A domain does not modify the transformation suppressive activity of KS1, whereas deletion of R2 abolishes this function. Thus, KS1 is a novel growth factor-inducible zinc finger transcriptional repressor protein with the potential to protect against neoplastic transformation induced by several oncogenes.
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Affiliation(s)
- B Gebelein
- Department of Molecular Neuroscience, Gastroenterology Research Unit, Mayo Clinic, Rochester, Minnesota 55905, USA
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47
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Katan-Khaykovich Y, Shaul Y. RFX1, a single DNA-binding protein with a split dimerization domain, generates alternative complexes. J Biol Chem 1998; 273:24504-12. [PMID: 9733744 DOI: 10.1074/jbc.273.38.24504] [Citation(s) in RCA: 24] [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
The transcription of various viral and cellular genes is regulated by palindromic and nonpalindromic DNA sites resembling the EP element of the hepatitis B virus enhancer, which generate similar DNA-protein complexes. The upper EP complex contains homodimers of the transcription regulator RFX1. We show that RFX1 possesses a split, extended dimerization domain composed of several evolutionarily conserved boxes, one of which was previously shown to mediate dimerization. Such an unusually long and complex dimerization domain could potentially serve for generating multiple complexes. In addition to the previously characterized complex, RFX1 generated a novel DNA-protein complex of extremely low mobility, formed only with palindromic DNA sites. Different deletions within the dimerization domain altered the relative abundance of the two complexes, suggesting an interplay between them. Formation of the low mobility complex correlated with transcriptional repression, in that both activities were mediated by several portions of the conserved region. Our results propose a mechanism by which the extended dimerization domain mediates the formation of alternative homodimeric complexes, which differ in the nature of the intersubunit interaction. By participating in different types of interactions, this domain may regulate the relative abundance of the different complexes, thus affecting transcriptional activity.
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Affiliation(s)
- Y Katan-Khaykovich
- Department of Molecular Genetics, The Weizmann Institute of Science, Rehovot 76100, Israel
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48
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Orlando V, Jane EP, Chinwalla V, Harte PJ, Paro R. Binding of trithorax and Polycomb proteins to the bithorax complex: dynamic changes during early Drosophila embryogenesis. EMBO J 1998; 17:5141-50. [PMID: 9724650 PMCID: PMC1170842 DOI: 10.1093/emboj/17.17.5141] [Citation(s) in RCA: 155] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
In Drosophila, the maintenance of developmentally important transcription patterns is controlled at the level of chromatin structure. The Polycomb group (PcG) and trithorax group (trxG) genes encode proteins involved in chromatin remodelling. PcG genes have been proposed to act by packaging transcriptional repressed chromosomal domains into condensed heterochromatin-like structures. Some of the trxG proteins characterized so far are members of chromatin opening complexes (e.g. SWI/SNF and GAGA/NURF) which facilitate binding of transcription factors and components of the basal transcriptional machinery. Genetic and biochemical data suggest that these two groups of regulatory factors may act through a common set of DNA elements. In the present study, we have investigated the binding of Trithorax (TRX) and Polycomb (PC) protein in the bithorax complex (BX-C) during embryogenesis. In addition, we have identified the minimal fragments from the Ultrabithorax (Ubx) regulatory region that are capable of recruiting TRX to chromosomal sites containing them. Comparative analysis of the binding of the two proteins shows that TRX and PC bind target sequences (PcG-regulated elements, PREs) by cellular blastoderm, when BX-C transcription begins. At the same stage, TRX but not PC is strongly associated with core promoters. Later, at germ band extension, the time of derepression in Polycomb mutants, PC binding is also detected outside core PREs and additionally binds to the fragments containing promoters.
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Affiliation(s)
- V Orlando
- ZMBH, University of Heidelberg, INF 282, 69120 Heidelberg, Germany
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49
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Okamoto T, Yamamoto S, Watanabe Y, Ohta T, Hanaoka F, Roeder RG, Ohkuma Y. Analysis of the role of TFIIE in transcriptional regulation through structure-function studies of the TFIIEbeta subunit. J Biol Chem 1998; 273:19866-76. [PMID: 9677423 DOI: 10.1074/jbc.273.31.19866] [Citation(s) in RCA: 46] [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 general transcription factor TFIIE plays important roles at two distinct but sequential steps in transcription as follows: preinitiation complex formation and activation (open complex formation), and the transition from initiation to elongation. The large subunit of human TFIIE (TFIIEalpha) binds to and facilitates the enzymatic functions of TFIIH, but TFIIE also functions independently from TFIIH. To determine functional roles of the small subunit of human TFIIE (TFIIEbeta), deletion mutations were systematically introduced into putative structural motifs and characteristic sequences. Here we show that all of these structures that lie within the central 227-amino acid region of TFIIEbeta are necessary and sufficient for both basal and activated transcription. We further demonstrate that two C-terminal basic regions are essential for physical interaction with both TFIIEalpha and single-stranded DNA, as well as with other transcription factors including the Drosophila transcriptional regulator Krüppel. In addition, we analyzed the effects of the TFIIEbeta deletion mutations on TFIIH-dependent phosphorylation of the C-terminal domain of RNA polymerase II and on wild type TFIIEbeta-driven basal transcription. Both responsible regions also mapped within the essential 227-amino acid region. Our results suggest that TFIIE engages in communication with both transcription factors and promoter DNA via the TFIIEbeta subunit.
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Affiliation(s)
- T Okamoto
- Institute for Molecular and Cellular Biology, Osaka University, Suita, Osaka 565-0871, Japan
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50
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Pardee TS, Bangur CS, Ponticelli AS. The N-terminal region of yeast TFIIB contains two adjacent functional domains involved in stable RNA polymerase II binding and transcription start site selection. J Biol Chem 1998; 273:17859-64. [PMID: 9651390 DOI: 10.1074/jbc.273.28.17859] [Citation(s) in RCA: 74] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The general transcription factor IIB (TFIIB) is required for accurate and efficient transcription of protein-coding genes by RNA polymerase II (RNAPII). To define functional domains in the highly conserved N-terminal region of TFIIB, we have analyzed 14 site-directed substitution mutants of yeast TFIIB for their ability to support cell viability, transcription in vitro, accurate start site selection in vitro and in vivo, and to form stable complexes with purified RNAPII in vitro. Mutations impairing the formation of stable TFIIB.RNAPII complexes mapped to the zinc ribbon fold, whereas mutations conferring downstream shifts in transcription start site selection were identified at multiple positions within a highly conserved homology block adjacent and C-terminal to the zinc ribbon. These results demonstrate that the N-terminal region of yeast TFIIB contains two separable and adjacent functional domains involved in stable RNAPII binding and transcription start site selection, suggesting that downstream shifts in transcription start site selection do not result from impairment of stable TFIIB.RNAPII binding. We discuss models for yeast start site selection in which TFIIB may affect the ability of preinitiation complexes to interact with downstream DNA or to affect start site recognition by a scanning polymerase.
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Affiliation(s)
- T S Pardee
- Department of Biochemistry and the Center for Advanced Molecular Biology and Immunology, School of Medicine and Biomedical Sciences, State University of New York, Buffalo New York 14214-3000, USA
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