Targeted Recruitment of Rpd3 Histone Deacetylase Represses Transcription by Inhibiting Recruitment of Swi/Snf, SAGA, and TATA Binding Protein

ABSTRACT Certain DNA-binding repressors inhibit transcription by recruiting Rpd3 histone deacetylase complexes to promoters and generating domains of histone deacetylation that extend over a limited number of nucleosomes. Here, we show that the degree of Rpd3-dependent repression depends on the activator and the level of activation, not the extent of histone deacetylation. In all cases tested, activator binding is unaffected by histone deacetylation. In contrast, Rpd3-dependent repression is associated with decreased occupancy by TATA binding protein (TBP), the Swi/Snf nucleosome-remodeling complex, and the SAGA histone acetylase complex. Transcriptional repression is bypassed by direct recruitment of TBP and several TBP-associated factors, but not by natural activation domains or direct recruitment of polymerase II holoenzyme components. These results suggest that the domain of localized histone deacetylation generated by recruitment of Rpd3 mediates repression by inhibiting recruitment of chromatin-modifying activities and TBP.

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A Human TATA Binding Protein-Related Protein with Altered DNA Binding Specificity Inhibits Transcription from Multiple Promoters and Activators

Molecular and Cellular Biology ◽

10.1128/mcb.19.11.7610 ◽

1999 ◽

Vol 19 (11) ◽

pp. 7610-7620 ◽

Cited By ~ 66

Author(s):

Paul A. Moore ◽

Josef Ozer ◽

Moreh Salunek ◽

Gwenael Jan ◽

Dennis Zerby ◽

...

Keyword(s):

Dna Binding ◽

Transcriptional Repression ◽

Transcription Initiation ◽

Binding Protein ◽

Tata Binding Protein ◽

Related Protein ◽

Multiple Promoters ◽

Binding Surface

ABSTRACT The TATA binding protein (TBP) plays a central role in eukaryotic and archael transcription initiation. We describe the isolation of a novel 23-kDa human protein that displays 41% identity to TBP and is expressed in most human tissue. Recombinant TBP-related protein (TRP) displayed barely detectable binding to consensus TATA box sequences but bound with slightly higher affinities to nonconsensus TATA sequences. TRP did not substitute for TBP in transcription reactions in vitro. However, addition of TRP potently inhibited basal and activated transcription from multiple promoters in vitro and in vivo. General transcription factors TFIIA and TFIIB bound glutathioneS-transferase–TRP in solution but failed to stimulate TRP binding to DNA. Preincubation of TRP with TFIIA inhibited TBP-TFIIA-DNA complex formation and addition of TFIIA overcame TRP-mediated transcription repression. TRP transcriptional repression activity was specifically reduced by mutations in TRP that disrupt the TFIIA binding surface but not by mutations that disrupt the TFIIB or DNA binding surface of TRP. These results suggest that TFIIA is a primary target of TRP transcription inhibition and that TRP may modulate transcription by a novel mechanism involving the partial mimicry of TBP functions.

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Targeted Recruitment of the Sin3-Rpd3 Histone Deacetylase Complex Generates a Highly Localized Domain of Repressed Chromatin In Vivo

Molecular and Cellular Biology ◽

10.1128/mcb.18.9.5121 ◽

1998 ◽

Vol 18 (9) ◽

pp. 5121-5127 ◽

Cited By ~ 197

Author(s):

David Kadosh ◽

Kevin Struhl

Keyword(s):

Dna Binding ◽

Histone Deacetylase ◽

Chromatin Structure ◽

Transcriptional Repression ◽

Dna Binding Proteins ◽

Histone Deacetylation ◽

Yeast Cells ◽

Multiprotein Complex ◽

Eukaryotic Organisms

ABSTRACT Eukaryotic organisms contain a multiprotein complex that includes Rpd3 histone deacetylase and the Sin3 corepressor. The Sin3-Rpd3 complex is recruited to promoters by specific DNA-binding proteins, whereupon it represses transcription. By directly analyzing the chromatin structure of a repressed promoter in yeast cells, we demonstrate that transcriptional repression is associated with localized histone deacetylation. Specifically, we observe decreased acetylation of histones H3 and H4 (preferentially lysines 5 and 12) that depends on the DNA-binding repressor (Ume6), Sin3, and Rpd3. Mapping experiments indicate that the domain of histone deacetylation is highly localized, occurring over a range of one to two nucleosomes. Taken together with previous observations, these results define a novel mechanism of transcriptional repression which involves targeted recruitment of a histone-modifying activity and localized perturbation of chromatin structure.

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Immunopurification of yeast TATA-binding protein and associated factors. Presence of transcription factor IIIB transcriptional activity

Journal of Biological Chemistry ◽

10.1016/s0021-9258(18)82256-6 ◽

1993 ◽

Vol 268 (21) ◽

pp. 15325-15328

Author(s):

D. Poon ◽

P.A. Weil

Keyword(s):

Transcription Factor ◽

Associated Factors ◽

Transcriptional Activity ◽

Binding Protein ◽

Tata Binding Protein ◽

Transcription Factor Iiib

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The Rpd3-Sin3 Histone Deacetylase Regulates Replication Timing and Enables Intra-S Origin Control in Saccharomyces cerevisiae

Molecular and Cellular Biology ◽

10.1128/mcb.24.11.4769-4780.2004 ◽

2004 ◽

Vol 24 (11) ◽

pp. 4769-4780 ◽

Cited By ~ 108

Author(s):

Jennifer G. Aparicio ◽

Christopher J. Viggiani ◽

Daniel G. Gibson ◽

Oscar M. Aparicio

Keyword(s):

Saccharomyces Cerevisiae ◽

Histone Deacetylase ◽

Transcriptional Repression ◽

Replication Timing ◽

Histone Deacetylation ◽

Origin Firing ◽

Replication Checkpoint ◽

Genome Transcription ◽

Late Origin

ABSTRACT The replication of eukaryotic genomes follows a temporally staged program, in which late origin firing often occurs within domains of altered chromatin structure(s) and silenced genes. Histone deacetylation functions in gene silencing in some late-replicating regions, prompting an investigation of the role of histone deacetylation in replication timing control in Saccharomyces cerevisiae. Deletion of the histone deacetylase Rpd3 or its interacting partner Sin3 caused early activation of late origins at internal chromosomal loci but did not alter the initiation timing of early origins or a late-firing, telomere-proximal origin. By delaying initiation relative to the earliest origins, Rpd3 enables regulation of late origins by the intra-S replication checkpoint. RPD3 deletion suppresses the slow S phase of clb5Δ cells by enabling late origins to fire earlier, suggesting that Rpd3 modulates the initiation timing of many origins throughout the genome. Examination of factors such as Ume6 that function together with Rpd3 in transcriptional repression indicates that Rpd3 regulates origin initiation timing independently of its role in transcriptional repression. This supports growing evidence that for much of the S. cerevisiae genome transcription and replication timing are not linked.

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Recruitment of TATA-Binding Protein–TAFI Complex SL1 to the Human Ribosomal DNA Promoter Is Mediated by the Carboxy-Terminal Activation Domain of Upstream Binding Factor (UBF) and Is Regulated by UBF Phosphorylation

Molecular and Cellular Biology ◽

10.1128/mcb.19.4.2872 ◽

1999 ◽

Vol 19 (4) ◽

pp. 2872-2879 ◽

Cited By ~ 51

Author(s):

JoAnn C. Tuan ◽

Weiguo Zhai ◽

Lucio Comai

Keyword(s):

Dna Binding ◽

Ribosomal Dna ◽

Transcriptional Activation ◽

Direct Contact ◽

Binding Protein ◽

Tata Binding Protein ◽

Rrna Synthesis ◽

Binding Factor ◽

Upstream Binding Factor ◽

Carboxy Terminal

ABSTRACT Human rRNA synthesis by RNA polymerase I requires at least two auxiliary factors, upstream binding factor (UBF) and SL1. UBF is a DNA binding protein with multiple HMG domains that binds directly to the CORE and UCE elements of the ribosomal DNA promoter. The carboxy-terminal region of UBF is necessary for transcription activation and has been shown to be extensively phosphorylated. SL1, which consists of TATA-binding protein (TBP) and three associated factors (TAFIs), does not have any sequence-specific DNA binding activity, and its recruitment to the promoter is mediated by specific protein interactions with UBF. Once on the promoter, the SL1 complex makes direct contact with the DNA promoter and directs promoter-specific initiation of transcription. To investigate the mechanism of UBF-dependent transcriptional activation, we first performed protein-protein interaction assays between SL1 and a series of UBF deletion mutants. This analysis indicated that the carboxy-terminal domain of UBF, which is necessary for transcriptional activation, makes direct contact with the TBP-TAFI complex SL1. Since this region of UBF can be phosphorylated, we then tested whether this modification plays a functional role in the interaction with SL1. Alkaline phosphatase treatment of UBF completely abolished the ability of UBF to interact with SL1; moreover, incubation of the dephosphorylated UBF with nuclear extracts from exponentially growing cells was able to restore the UBF-SL1 interaction. In addition, DNase I footprinting analysis and in vitro-reconstituted transcription assays with phosphatase-treated UBF provided further evidence that UBF phosphorylation plays a critical role in the regulation of the recruitment of SL1 to the ribosomal DNA promoter and stimulation of UBF-dependent transcription.

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Correction: A highly conserved ATPase protein as a mediator between acidic activation domains and the TATA-binding protein

Nature ◽

10.1038/379658a0 ◽

1996 ◽

Vol 379 (6566) ◽

pp. 658-658 ◽

Cited By ~ 12

Author(s):

Jonathan C. Swaffield ◽

Karsten Melcher ◽

Stephen Albert Johnston

Keyword(s):

Binding Protein ◽

Tata Binding Protein ◽

Activation Domains

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Abstract P221: Retinoblastoma Protein--Associated Proteins 48 and 46 Are Novel p300/GATA4-Binding Partners Involved in Hypertrophic Responses in Cardiomyocytes

Circulation Research ◽

10.1161/res.109.suppl_1.ap221 ◽

2011 ◽

Vol 109 (suppl_1) ◽

Author(s):

Yoichi Sunagawa ◽

Yasufumi Katanasaka ◽

Taishi Terada ◽

Yuichi Watanabe ◽

Hiromichi Wada ◽

...

Keyword(s):

Transcriptional Activation ◽

Transcriptional Repression ◽

Zinc Finger Protein ◽

Retinoblastoma Protein ◽

Histone Deacetylation ◽

Hek293 Cells ◽

Functional Protein ◽

Nucleosome Remodeling ◽

Transcriptional Activation Domain ◽

Functional Relationships

Background: A zinc finger protein GATA4 is one of hypertrophy-responsive transcription factors, and increases its DNA-binding and transcriptional activities in response to hypertrophic stimuli in cardiomyocytes. Activation of GATA4 during this process is mediated, in part, through acetylation by intrinsic histone acetyltransferases such as a transcriptional coactivator p300. Here, we show that retinoblastoma protein (Rb)-associated protein 48 and 46 (RbAp48, RbAp46), components of NuRD (nucleosome remodeling and deacetylase) complex that has been implicated in chromatin remodeling and transcriptional repression associated with histone deacetylation, are novel components of p300/GATA4 complex. However, the precise functional relationships among p300, GATA4, RbAp48, and RbAp46 remain unknown. Methods and Results: A series of GST pull-down assays revealed that the C-terminal domain of RbAp48/46 bound to the N-terminal transcriptional activation domain of GATA4 and C/H-3 domain of p300, respectively. Immunoprecipitation followed by western blotting demonstrated that RbAp48/46 repressed p300-induced acetylation of GATA4 and histones. While overexpressions of RbAp48/46 inhibited p300/GATA4-induced atrial natriuretic factors (ANF) and endotheline-1 (ET-1) promoter activities, knockdown of neither RbAp48 nor RbAp46 by RNAi enhanced these promoter activities in HEK293 cells. Stimulation of cardiomyocytes with phenylephrine (PE) decreased the binding of GATA4/p300 with RbAp48/46. RbAp48/46 repressed PE-induced hypertrophic responses such as myofibrillar organization, increase in cell size and promoter activation of the ANF and ET-1 in cardiomyocytes. Conclusion: These findings demonstrate that RbAp48 and RbAp46 form a functional protein complex with GATA4/p300 and regulated hypertrophic responses in cardiomyocytes.

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