Structural similarity between TAFs and the heterotetrameric core of the histone octamer

Xie, Xin; Kokubo, Tetsuro; Cohen, Steven L.; Mirza, Urooj A.; Hoffmann, Alexander; Chait, Brian T.; Roeder, Robert G.; Nakatani, Yoshihiro; Burley, S.K.

doi:10.1038/380316a0

Cited by 250 publications

(225 citation statements)

References 45 publications

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“…Histones H2A, H2B, H3, and H4 all contain histone folds (51), as do the yeast HAP3 and HAP5 activator proteins (CBF proteins in mammals; ref. 52) and several TAF II s (45,46). These TAF II s and histones are able to interact with each other in vitro through their histone fold regions (45).…”

Section: Discussionmentioning

confidence: 99%

Functional antagonism between RNA polymerase II holoenzyme and global negative regulator NC2 in vivo

Gadbois

Chao

Reese

et al. 1997

Proc. Natl. Acad. Sci. U.S.A.

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Activation of eukaryotic class II gene expression involves the formation of a transcription initiation complex that includes RNA polymerase II, general transcription factors, and SRB components of the holoenzyme. Negative regulators of transcription have been described, but it is not clear whether any are general repressors of class II genes in vivo. We reasoned that defects in truly global negative regulators should compensate for deficiencies in SRB4 because SRB4 plays a positive role in holoenzyme function. Genetic experiments reveal that this is indeed the case: a defect in the yeast homologue of the human negative regulator NC2 (Dr1⅐DRAP1) suppresses a mutation in SRB4. Global defects in mRNA synthesis caused by the defective yeast holoenzyme are alleviated by the NC2 suppressing mutation in vivo, indicating that yeast NC2 is a global negative regulator of class II transcription. These results imply that relief from repression at class II promoters is a general feature of gene activation in vivo.Activation of class II gene transcription in eukaryotes involves the recruitment of a transcription initiation complex that includes the RNA polymerase II holoenzyme (1-6). The yeast RNA polymerase II holoenzyme is a large multisubunit complex containing RNA polymerase II, a subset of the general transcription factors, and SRB regulatory proteins (7-11). Mammalian RNA polymerase II holoenzymes have also been purified, and an SRB7 homologue has been identified as a component of those complexes (12)(13)(14).For some class II genes, regulation appears to involve both positive and negative transcriptional regulators. The negative regulators that have been described include proteins purified for their ability to inhibit transcription in vitro (15-21) and genes identified because their products repress transcription from a subset of class II genes in vivo (21-29). For example, the human proteins NC1 (15, 16), NC2 or Dr1⅐DRAP1 (16,17,20), and DNA topoisomerase I (18, 19) repress basal transcription in vitro. The products of the yeast genes MOT1 (21-24), NOT1-4 (25-27), and SIN4 (28-29) negatively regulate at least a subset of yeast genes in vivo. Whether any of these negative regulators are generally employed for class II gene regulation in vivo is not yet clear.The RNA polymerase II C-terminal domain and the associated SRB complex have been implicated in the response to transcriptional activators (7-9, 30, 31). Two holoenzyme components, SRB4 and SRB6, have been shown to play essential and positive roles in transcription at the majority of class II genes in Saccharomyces cerevisiae (32). We reasoned that a defect in SRB4 might be alleviated by defects in general negative regulators and that knowledge of such regulators could contribute to our understanding of the mechanisms involved in gene regulation in vivo. Here we show that a deficiency in yeast NC2 can compensate for the global transcriptional defects caused by mutations in the SRB4 and SRB6 subunits of the RNA polymerase II holoenzyme and that NC2 is a globa...

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Section: Discussionmentioning

confidence: 99%

Functional antagonism between RNA polymerase II holoenzyme and global negative regulator NC2 in vivo

Gadbois

Chao

Reese

et al. 1997

Proc. Natl. Acad. Sci. U.S.A.

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“…This core structure was suggested to depend upon the HFD, a structural motif shared by the core histones (22) and many other proteins (70). Nine of 14 yeast Tafps appear to contain HFDs, and subsets of these can form dimers with specific partner HFD Tafps (3,6,9,23,24,29,45,47,80). Indeed, Tan and colleagues (66) have described the formation and characterization of such an octameric complex comprised of four HFD-Tafps, a dimer of Taf6p-Taf9p bound to a dimer of Taf4p-Taf12p.…”

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confidence: 99%

Molecular and Genetic Characterization of a Taf1p Domain Essential for Yeast TFIID Assembly

Singh

Bland

Weil

2004

Molecular and Cellular Biology

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Yeast Taf1p is an integral component of the multiprotein transcription factor TFIID. By using coimmunoprecipitation assays, coupled with a comprehensive set of deletion mutants encompassing the entire open reading frame of TAF1, we have discovered an essential role of a small portion of yeast Taf1p. This domain of Taf1p, termed region 4, consisting of amino acids 200 to 303, contributes critically to the assembly and stability of the 15-subunit TFIID holocomplex. Region 4 of Taf1p is mutationally sensitive, can assemble several Tafps into a partial TFIID complex, and interacts directly with Taf4p and Taf6p. Mutations in Taf1p-region 4 induce temperature-conditional growth of yeast cells. At the nonpermissive temperature these mutations have drastic effects on both TFIID integrity and mRNA synthesis. These data are consistent with the hypothesis that Taf1p subserves a critical scaffold function within the TFIID complex. The significance of these data with regard to TFIID structure and function is discussed.TFIID, one of several multiprotein general transcription factors required for RNA polymerase II (PolII)-catalyzed mRNA gene transcription, is comprised of the TATA-binding protein (TBP) and 14 distinct TBP-associated factors (TAFs or Tafps) that range in M r from 17,000 to 150,000 in Saccharomyces cerevisiae (62,63,65,75). These TFIID subunits share significant sequence conservation with their metazoan orthologs (1,22,26). In vitro, PolII needs six general transcription factors, TFIIA, -B, -D, -E, -F, and -H, to form functional preinitiation complexes (PICs) (12, 51, 54); TFIID plays several critical roles in this process. First, TFIID functions during promoter recognition by binding directly to the promoter (67,76,77). On promoters containing a TATA box, Tafps help stabilize TBP binding to the TATA element via interaction with TATA-proximal initiator DNA sequences (69). Tafp-DNA interactions may be particularly important for TFIID binding to promoters that lack a canonical TATA element and contain TATA-proximal initiator and distal promoter element sequences (13,15,42,69,76). Second, Tafps can function as coactivators during transcriptional activation by making direct contacts with specific activators leading to an increase in PolII PIC formation (1, 16). Finally, Taf1p contains several distinct enzymatic activities, those of histone acetyltransferase (HAT) (46), protein kinase (19), and ubiquitin ligase (55). These enzymatic activities presumably modify proteins that stimulate PIC formation and/or function, leading to PolII transcription initiation.In most contexts, the Tafp subunits of TFIID are essential for survival, as Tafp inactivation or depletion results in cessation of specific mRNA synthesis and loss of cell viability (3,4,33,34,56,59,64,65,78). Because of these critical roles, the composition, organization, assembly, structure, and function of the TFIID complex have been topics of great interest. TBP appears to be incorporated into the TFIID complex primarily through its interaction with the biparti...

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“…The nomenclature for these interaction surfaces was first defined for the histone-like TAF42/62 complex whose structure was determined before the nucleosome (Xie et al 1996). A number of other protein complexes have since been shown to share the same histone fold complex structure, although not all of these necessarily bind DNA (Kamada et al 2001;Hartlepp et al 2005;Nishino et al 2012).…”

Section: Histone Octamer Is a Scaffold For Dna Contactsmentioning

confidence: 99%

Principles and practice of nucleosome positioningin vitro

Flaus

2011

Frontiers in Life Science

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Structural similarity between TAFs and the heterotetrameric core of the histone octamer

Cited by 250 publications

References 45 publications

Functional antagonism between RNA polymerase II holoenzyme and global negative regulator NC2 in vivo

Functional antagonism between RNA polymerase II holoenzyme and global negative regulator NC2 in vivo

Molecular and Genetic Characterization of a Taf1p Domain Essential for Yeast TFIID Assembly

Principles and practice of nucleosome positioningin vitro

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