Dynamic interplay of TFIIA, TBP and TATA DNA

Weideman, C A; Netter, R C; Benjamin, Lawrence R.; McAllister, Janette; Schmiedekamp, L A; Coleman, Robert A.; Pugh, B. Franklin

doi:10.1006/jmbi.1997.1152

Cited by 54 publications

(60 citation statements)

References 61 publications

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“…This is entirely consistent with previous investigations (19,20) showing reduced affinity and stability of TBP for TATA mutants compared with TATA (21). Thus, our data predict that TFIIA is more important on TATA-containing promoters than on TATA-less promoters.…”

Section: Discussionsupporting

confidence: 93%

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Efficient Binding of NC2·TATA-binding Protein to DNA in the Absence of TATA

Gilfillan¹,

Stelzer²,

Piaia³

et al. 2005

Journal of Biological Chemistry

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Negative cofactor 2 (NC2) forms a stable complex with TATA-binding protein (TBP) on promoters. This prevents the assembly of transcription factor (TF) IIA and TFIIB and leads to repression of RNA polymerase II transcription. Here we have revisited the interactions of NC2⅐TBP with DNA. We show that NC2⅐TBP complexes exhibit a significantly reduced preference for TATA box sequences compared with TBP and TBP⅐TFIIA complexes. In chromatin immunoprecipitations, NC2 is found on a variety of human TATAcontaining and TATA-less promoters. Substantial amounts of NC2 are present in a complex with TBP in bulk chromatin. A complex of NC2⅐TBP displays a K D for DNA of ϳ2 ؋ 10 ؊9 M for a 35-bp major late promoter oligonucleotide. While preferentially recognizing promoter-bound TBP, NC2 also accelerates TBP binding to promoters and stabilizes TBP⅐DNA complexes. Our data suggest that NC2 controls TBP binding and maintenance on DNA that is largely independent of a canonical TATA sequence.TATA-binding protein (TBP) 1 binds to eukaryotic promoters to nucleate initiation of transcription (1-3). The crystal structure of the TBP⅐DNA complex revealed a saddle-shaped conformation of TBP in which the highly conserved carboxyl terminus forms a concave surface that interacts with the minor groove of DNA. As a consequence, the minor groove becomes dramatically widened, and the DNA is severely bent (4). The characteristic bend as well as the TBP conformation is conserved in the co-crystal structures of TBP⅐TFIIA⅐DNA (5, 6), TBP⅐TFIIB⅐DNA (7), and TBP⅐NC2⅐DNA (8).The thermodynamics and kinetics of TBP-TATA interactions have been investigated in detail. Both yeast and human TBP show specificity for TATA boxes. Values for the K D are in the range of 5 ϫ 10 Ϫ10 to 2 ϫ 10 Ϫ8 M for yeast TBP (9 -13) and 4.6 ϫ 10 Ϫ10 to 1 ϫ 10 Ϫ9 M for human TBP (14, 15). Variations may be accounted for in part by the specific conditions and the different methods employed, which are gel shifts and footprints versus solution FRET studies. Specificities of TBP for TATA range from Ͻ1 order of magnitude if a canonical TATA is compared with single point mutants in the TATA sequence to roughly 3 orders of magnitude relative to random DNA (14). Human TBP has been proposed to bind DNA through the conserved domain in the usual specific manner or, alternatively, in a nonspecific manner that depends on its non-conserved amino-terminal region (16).Several factors modulate binding of TBP to DNA. The TBPassociated factors (TAFs) support binding of TBP specifically to TATA-less promoters via DNA contacts through cognate promoter sequences (17, 18). The general transcription factor TFIIA accelerates and stabilizes binding of TBP to TATA boxes (19 -21). It also functions as a co-activator for some transcriptional activators (22-26). TFIIA further functions as an antagonist of NC2 (also called Dr1/DRAP) (27, 28). Evidence for this equilibrium between NC2 and TFIIA stems from both biochemical investigations in human cells and genetic studies in yeast in which mutants in TFIIA genes w...

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Section: Discussionsupporting

confidence: 93%

“…B, NC2 accelerates binding of TBP to DNA. Samples were incubated for increasing time periods (1,3,10,20,40, and 50 min), 2.5 nM 35-bp AdML promoter. The first half of the gel contains TBP (32 nM), and the second half contains TBP and NC2 (8 and 2.2 nM, respectively).…”

Section: Discussionmentioning

confidence: 99%

Efficient Binding of NC2·TATA-binding Protein to DNA in the Absence of TATA

Gilfillan¹,

Stelzer²,

Piaia³

et al. 2005

Journal of Biological Chemistry

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“…The effect of TFIIA on the stability of TBP/ TATA complexes was anticipated from the previous work of Pugh and colleagues, who found that human TFIIA increased the stability of TBP/TATA complexes by tenfold. 25 The most profound effect that we observed was the 55-fold kinetic stabilization of complexes formed on the non-consensus TATA(A3) DNA. Our work shows that TFIIA not only stabilizes TBP/TATA complexes, but also leads us to propose a model in which TFIIA locks the TATA DNA into a uniform bent state regardless of the salt concentration or the sequence of the TATA box.…”

Section: Tbp Binding and Bending Of Tata Dna As Measured By Quantitatmentioning

confidence: 82%

“…[24][25][26] Human TFIIA is a three-subunit protein totaling 69 kDa and is believed to be required for transcription at most eukaryotic promoters. [27][28][29][30] It has been shown to interact with multiple activators, TBP associated factors (TAFs), and general transcription factors, including TBP.…”

Section: Introductionmentioning

confidence: 99%

TFIIA Changes the Conformation of the DNA in TBP/TATA Complexes and Increases their Kinetic Stability

Hieb

Halsey

Betterton

et al. 2007

Journal of Molecular Biology

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“…In contrast, factors such as Mot1 or the Taf1 N-terminal domain (TAND) inhibit the DNA binding activity of TBP (Auble et al 1994;Kokubo et al 1998;Cang et al 1999). The general factor TFIIA interacts directly with TBP and stabilizes TBP-DNA interactions (Weideman et al 1997;Hampsey 1998;Liu et al 1999). TFIIA also stimulates and stabilizes the binding of TFIID to DNA as part of an activator-TFIID-TFIIA-DNA complex, a rate-limiting intermediate in the transcription of certain promoters (Wang et al 1992;Lieberman and Berk 1994;Chi et al 1995).…”

mentioning

confidence: 99%

Positive and negative functions of the SAGA complex mediated through interaction of Spt8 with TBP and the N-terminal domain of TFIIA

Warfield

Ranish²,

Hahn³

2004

Genes Dev.

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A surface that is required for rapid formation of preinitiation complexes (PICs) was identified on the N-terminal domain (NTD) of the RNA Pol II general transcription factor TFIIA. Site-specific photocross-linkers and tethered protein cleavage reagents positioned on the NTD of TFIIA and assembled in PICs identified the SAGA subunit Spt8 and the TFIID subunit Taf4 as located near this surface. In agreement with these findings, mutations in Spt8 and the TFIIA NTD interact genetically. Using purified proteins, it was found that TFIIA and Spt8 do not stably bind to each other, but rather both compete for binding to TBP. Consistent with this competition, Spt8 inhibits the binding of SAGA to PICs in the absence of activator. In the presence of activator, Spt8 enhances transcription in vitro, and the positive function of the TFIIA NTD is largely mediated through Spt8. Our results suggest a mechanism for the previously observed positive and negative effects of Spt8 on transcription observed in vivo.[Keywords: Transcription; SAGA; TFIIA; coactivator; repression] Supplemental material is available at http://www.genesdev.org.

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Dynamic interplay of TFIIA, TBP and TATA DNA

Cited by 54 publications

References 61 publications

Efficient Binding of NC2·TATA-binding Protein to DNA in the Absence of TATA

Efficient Binding of NC2·TATA-binding Protein to DNA in the Absence of TATA

TFIIA Changes the Conformation of the DNA in TBP/TATA Complexes and Increases their Kinetic Stability

Positive and negative functions of the SAGA complex mediated through interaction of Spt8 with TBP and the N-terminal domain of TFIIA

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