The DPE, a Conserved Downstream Core Promoter Element That Is Functionally Analogous to the TATA Box

Burke, Thomas W.; Willy, Patricia J.; Kutach, Alan K.; Butler, Jennifer E.F.; Kadonaga, James T.

doi:10.1101/sqb.1998.63.75

Cited by 63 publications

(42 citation statements)

References 37 publications

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“…In this review, we define the core promoter as the minimal stretch of contiguous DNA sequence that is sufficient to direct accurate initiation of transcription by the RNA polymerase II machinery (for review, see Struhl 1987;Weis and Reinberg 1992;Smale 1994Smale , 1997Smale , 2001Smale et al 1998;Burke et al 1998). Typically, the core promoter encompasses the site of transcription initiation and extends either upstream or downstream for an additional ∼ 35 nt.…”

Section: What Is the Core Promoter?mentioning

confidence: 99%

The RNA polymerase II core promoter: a key component in the regulation of gene expression

Butler¹,

Kadonaga²

2002

Genes Dev.

532

433

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Section: What Is the Core Promoter?mentioning

confidence: 99%

The RNA polymerase II core promoter: a key component in the regulation of gene expression

Butler¹,

Kadonaga²

2002

Genes Dev.

532

433

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“…TATA-containing promoters can function in the absence of an Inr, whereas DPE promoters are Inr-dependent; TATA box directed transcription occurs on average 25-30 bp downstream of the TATA box while Inr driven transcription typically originates at the adenosine residue in the ϩ1 position of the Inr element itself (2). Sequence analysis of the Drosophila and human genomes indicates that only a minority of promoters contain the classical arrangement of one TATA box and one Inr element (3,4). The remaining promoters contain varying combinations of TATA, Inr, and DPE elements.…”

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confidence: 99%

Sequence and Spacing of TATA Box Elements Are Critical for Accurate Initiation from the β-Phaseolin Promoter

Grace

Chandrasekharan

Hall

et al. 2004

Journal of Biological Chemistry

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The ␤-phaseolin (phas) gene, which encodes one of the major seed storage proteins of P. vulgaris, is tightly regulated at the transcription level resulting in strict tissuespecific and spatial expression during embryonic development. The phas proximal promoter contains a complex arrangement of core promoter elements including three TATA boxes as well as several putative initiator elements. To delineate the respective contributions of the core promoter elements to transcription initiation we have performed site-directed mutagenesis of the phas promoter. In vivo expression studies were performed on transgenic Arabidopsis harboring phas promoter mutants driving expression of the ␤-glucuronidase (gus) reporter gene. Quantitative assessment of GUS activity in seeds bearing the promoter mutants indicated that both sequence and spacing of the TATA elements influenced the efficiency of transcription. Substitution, insertion or deletion mutations had no effect on histochemical staining patterns indicating that strict spacing requirements are not essential for correct spatial expression of phas during embryogenesis. Further evaluation of the phas promoter by in vitro transcription analysis revealed the presence of multiple TATA-dependent transcription initiation start sites. The distance between TATA elements and transcription start sites was maintained in insertion and deletion mutants through the creation of novel initiation sites, indicating that positioning of the TATA elements rather than DNA sequence was the primary determinant of start site location. We conclude that, while dispensable for proper spatial distribution, the complex architecture of the phas promoter is required to ensure high levels of accurate phas transcription initiation in the developing embryo.The proximal promoter region of a gene contains core promoter elements that determine the basal transcription activity of the gene and typically direct the positioning of the transcription initiation start site. Three different classes of transcription initiation elements have been identified in eukaryotes: TATA boxes, initiator (Inr) 1 elements and downstream promoter elements (DPE). To date, only TATA boxes and Inr elements have been identified in plant promoters. All three elements utilize similar mechanisms of initiation requiring RNA polymerase II and sequence-specific binding of transcription factor IID (1). However, mechanistic differences exist between the different initiation elements. TATA-containing promoters can function in the absence of an Inr, whereas DPE promoters are Inr-dependent; TATA box directed transcription occurs on average 25-30 bp downstream of the TATA box while Inr driven transcription typically originates at the adenosine residue in the ϩ1 position of the Inr element itself (2). Sequence analysis of the Drosophila and human genomes indicates that only a minority of promoters contain the classical arrangement of one TATA box and one Inr element (3, 4). The remaining promoters contain varying combinations of TATA, Inr, and DPE ele...

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“…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).…”

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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 DPE, a Conserved Downstream Core Promoter Element That Is Functionally Analogous to the TATA Box

Cited by 63 publications

References 37 publications

The RNA polymerase II core promoter: a key component in the regulation of gene expression

The RNA polymerase II core promoter: a key component in the regulation of gene expression

Sequence and Spacing of TATA Box Elements Are Critical for Accurate Initiation from the β-Phaseolin Promoter

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

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