Drosophila TFIID binds to a conserved downstream basal promoter element that is present in many TATA-box-deficient promoters.

Burke, Thomas W.; Kadonaga, James T.

doi:10.1101/gad.10.6.711

Cited by 363 publications

(376 citation statements)

References 83 publications

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“…Of further complexity is the discovery of a ' downstream element ', typically 20-30 bases downstream from the transcription start site [37,38]. This motif, either weakly or strongly conserved in a number of genes, is apparently a binding site for another category of proteins and is essential for the quality and quantity of transcription in some genes [39], but the protein(s) binding to this site is\are even less understood than those binding at the initiator. In marked contrast to the above are those genes that apparently function without either a TATA box or an initiator element [40].…”

Section: Discussionmentioning

confidence: 99%

“…The third binding factor that is responsible is probably not that which binds to the ' downstream element ' described from a number of TATA-containing [37] and TATA-less promoters, including some insect genes ( [39] ; A\GGA\TCGTG). The JH esterase gene does possess a similar motif with close similarity to that element, and it is appropriately positioned about 30 bp downstream from the transcription start site ( +#% AGACATG +$!…”

Section: Discussionmentioning

confidence: 99%

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Transcription of the juvenile hormone esterase gene under the control of both an initiator and AT-rich motif

Jones

Mańczak

Schelling

et al. 1998

Biochemical Journal

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The binding of transcription factors to the core promoter of the juvenile hormone esterase gene was functionally characterized using both a cell-free in vitrotranscription functional assay and a cell transfection assay. A core JHE promoter (-61 to +28 bp relative to transcription start site) supported faithful transcription from the in vivo transcription start site. The nuclear extracts from the Sf9 insect cell line that provided transcription from that template also bound to that template as a probe in gel-mobility shift assays. Deletion or transversion of the initiator-binding motif (-1 to +4 bp) abolished detectable transcription either in vitro or in transfected cells. An AT-rich motif (ATATAT; -28 to -23 bp) serves another transcription factor-binding site. Mutation of the AT-rich motif to a canonical TATA-box preserved transcription, while either its deletion or complete transversion abolished or significantly reduced detectable transcriptional activity. These results indicate that, under these conditions, the functional operation of this core promoter approaches that of a composite promoter in which both the TATA- and initiator-binding protein complexes are necessary, even for basal transcription. On the other hand, these debilitating mutations to either the TATA box or initiator motif did not prevent the ability of the corresponding gel-shift competitive probes to compete with the wild-type promoter for binding by the transcription factors. Even a double transversion of both the AT-rich motif and the initiator-binding motif was able to competitively displace the protein complex that bound to the labelled wild-type probe. These data strongly indicate the presence of (an) additional core-promoter-associated transcription factor(s) (that is not the ‘downstream element ’) that contact(s) the AT-binding complex and/or initiator-binding factor with sufficient avidity to remove them from binding to the competing wild-type promoter sequence.

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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Transcription of the juvenile hormone esterase gene under the control of both an initiator and AT-rich motif

Jones

Mańczak

Schelling

et al. 1998

Biochemical Journal

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“…The DPE was identified in a study of the binding of purified Drosophila TFIID to TATA-less core promoters (Burke and Kadonaga, 1996). The DPE is most commonly found in TATA-less promoters, although some promoters contain both DPE and TATA motifs (Kutach and Kadonaga, 2000).…”

Section: The Dpementioning

confidence: 99%

The DPE, a core promoter element for transcription by RNA polymerase II

Kadonaga

2002

Exp Mol Med

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Abbreviations: BRE, TFIIB recognition element; DPE, downstream core promoter element; Inr, initiator element; LINE, long interspersed nuclear element; NC2, negative cofactor 2 (NC2 is also known as Dr1-Drap1); nt, nucleotides; TAF, TBP-associated factor; TBP, TATA box-binding protein; TFIIB, RNA polymerase II basal transcription factor B; TFIID, RNA polymerase II basal transcription factor D. OverviewThe core promoter is an important yet often overlooked component in the regulation of transcription by RNA polymerase II. In fact, the core promoter is the ultimate target of action of all of the factors and coregulators that control the transcriptional activity of every gene. In this review, I describe our current knowledge of a downstream core promoter element termed the DPE, which is a TFIID recognition site that is conserved from Drosophila to humans. The DPE is located from +28 to +32 relative to the +1 transcription start site, and is mainly present in core promoters that lack a TATA box motif. Moreover, in Drosophila, the DPE appears to be about as common as the TATA box. There are distinct mechanisms of basal transcription from DPE-versus TATA-dependent core promoters. For instance, NC2/Dr1-Drap1 is a repressor of TATA-dependent transcription and an activator of DPE-dependent transcription. In addition, DPE-specific and TATA-specific transcriptional enhancers have been identified. These findings further indicate that the core promoter is an active participant in the regulation of eukaryotic gene expression.Keywords: DPE, TATA, Inr, core promoter, RNA polymerase II Regulation of Transcription by RNA Polymerase IIThe eukaryotic cell is confronted with the challenge of properly regulating each of its tens of thousands of genes. When it is considered that each gene has its own unique expression program, it becomes evident that the control of gene activity requires an enormous amount of resources in terms of information (i.e., instructions for the regulation of each gene) and effectors (i.e., factors that mediate the gene expression programs).Transcription is a key step at which gene activity is controlled. Much of the information that specifies the transcriptional program of a gene is encoded in its DNA sequence. These cis-acting sequences include enhancers, silencers, proximal promoter regions, core promoters, and boundary/insulator elements (see, for example: Struhl, 1987;Weis and Reinberg, 1992;Smale, 1994Smale, , 1997Smale, , 2001Blackwood and Kadonaga, 1998;Bulger and Groudine, 1999;Butler and Kadonaga, 2002;West et al., 2002). Enhancer and silencer elements contain recognition sites for a variety of sequence-specific DNA-binding factors, and can act from long distances (such as tens of kbp) from the transcription start site. The proximal promoter region also contains multiple recognition sites for sequence-specific DNA-binding factors, and is typically located from about -40 to about -250 relative to the +1 start site. The core promoter is generally located within -40 to +40 of the start site, and is recog...

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“…Underlines labelled Inr1 and Inr2, respectively, show initiators for 1/ 2 and 5/ 6 RNA starts. The underline labelled DPE is a downstream promoting element (Burke & Kadonaga 1996). Thin underlines V and A, respectively, indicates a 15-bp-long sequence invariant between D. melanogaster and D. virilis en genes and a region including a sequence conserved between en and inv.…”

Section: Assay Of Enhancer-dependent Promoter Activity In¯y Body-formmentioning

confidence: 99%

Identification of engrailed promoter elements essential for interactions with a stripe enhancer in Drosophila embryos

et al. 1999

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Drosophila TFIID binds to a conserved downstream basal promoter element that is present in many TATA-box-deficient promoters.

Cited by 363 publications

References 83 publications

Transcription of the juvenile hormone esterase gene under the control of both an initiator and AT-rich motif

Transcription of the juvenile hormone esterase gene under the control of both an initiator and AT-rich motif

The DPE, a core promoter element for transcription by RNA polymerase II

Identification of engrailed promoter elements essential for interactions with a stripe enhancer in Drosophila embryos

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