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

Kadonaga, James T.

doi:10.1038/emm.2002.36

Cited by 97 publications

(68 citation statements)

References 71 publications

(64 reference statements)

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“…Conservation of a stability element at the 5Ј end of p742 transcripts would allow both classes of transcripts to be upregulated by the same mechanism. However, the location of essential DRE1 elements downstream of the core promoter does not exclude the possibility that the relevant elements are DNA elements, as transcription factor binding sites downstream of initiation sties are hardly rare, especially in multiple-start promoters (8,9,13,14,17,24,29,33,38,63).…”

Section: Discussionmentioning

confidence: 99%

Genetic Analysis of the Human Papillomavirus Type 31 Differentiation-Dependent Late Promoter

Bodily

Meyers

2005

J Virol

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Human papillomaviruses infect stratifying squamous epithelia, causing benign and malignant lesions. Upon differentiation of the host keratinocyte, the virus undergoes a dramatic increase in both DNA replication and transcription from the late promoter, leading to expression of late genes and virion morphogenesis. In human papillomavirus type 31 (HPV31), the late promoter is designated p742 and includes multiple start sites embedded within the E7 gene. In this report, we mapped viral DNA elements that control transcriptional activity from p742. Enhancer elements in the viral upstream regulatory region positively regulate this promoter. The region containing the transcriptional start sites is dispensable for activity, and at least two separate elements in the E6/E7 region are capable of supporting transcription. Of these, we mapped one to a 150-bp region of the E7 open reading frame and designate it the core p742 promoter. Using GF109203X, an inhibitor of protein kinase C signaling, we show that p742 activation is independent of viral genome amplification. Finally, we mapped elements in the region of p742 that confer responsiveness to differentiation and show that the upstream regulatory region does not contribute to the differentiation response of p742. These studies are an important step toward understanding the functioning and regulation of this multiple-start promoter.

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Section: Discussionmentioning

confidence: 99%

Genetic Analysis of the Human Papillomavirus Type 31 Differentiation-Dependent Late Promoter

Bodily

Meyers

2005

J Virol

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“…sequences (Kadonaga 2002). All three heterologous promoters gave dark pigmen-1999; Wray et al 2003).…”

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confidence: 98%

Enhancer Choice in Cis and in Trans in Drosophila melanogaster

Morris

Petrov²,

Lee

et al. 2004

Genetics

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Eukaryotic enhancers act over very long distances, yet still show remarkable specificity for their own promoter. To better understand mechanisms underlying this enhancer-promoter specificity, we used transvection to analyze enhancer choice between two promoters, one located in cis to the enhancer and the other in trans to the enhancer, at the yellow gene of Drosophila melanogaster. Previously, we demonstrated that enhancers at yellow prefer to act on the cis-linked promoter, but that mutation of core promoter elements in the cis-linked promoter releases enhancers to act in trans. Here, we address the mechanism by which these elements affect enhancer choice. We consider and explicitly test three models that are based on promoter competency, promoter pairing, and promoter identity. Through targeted gene replacement of the endogenous yellow gene, we show that competency of the cis-linked promoter is a key parameter in the cis-trans choice of an enhancer. In fact, complete replacement of the yellow promoter with both TATAcontaining and TATA-less heterologous promoters maintains enhancer action in cis.

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“…While TATA elements are used at a significant number of promoters in both S. cerevisiae and metazoans, the TATA-start site distance is fixed in metazoans but not in S. cerevisiae, and the start site itself is more conserved in metazoans (68). In addition, downstream promoter elements, widely used in metazoans, are not found in S. cerevisiae (40).…”

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confidence: 99%

Analysis of Transcriptional Activation at a Distance inSaccharomyces cerevisiae

Dobi

Winston

2007

Molecular and Cellular Biology

102

103

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Most fundamental aspects of transcription are conserved among eukaryotes. One striking difference between yeast Saccharomyces cerevisiae and metazoans, however, is the distance over which transcriptional activation occurs. In S. cerevisiae, upstream activation sequences (UASs) are generally located within a few hundred base pairs of a target gene, while in Drosophila and mammals, enhancers are often several kilobases away. To study the potential for long-distance activation in S. cerevisiae, we constructed and analyzed reporters in which the UAS-TATA distance varied. Our results show that UASs lose the ability to activate normal transcription as the UAS-TATA distance increases. Surprisingly, transcription does initiate, but proximally to the UAS, regardless of its location. To identify factors affecting long-distance activation, we screened for mutants allowing activation of a reporter when the UAS-TATA distance is 799 bp. These screens identified four loci, SIN4, SPT2, SPT10, and HTA1-HTB1, with sin4 mutations being the strongest. Our results strongly suggest that longdistance activation in S. cerevisiae is normally limited by Sin4 and other factors and that this constraint plays a role in ensuring UAS-core promoter specificity in the compact S. cerevisiae genome.Many aspects of transcription initiation are conserved between Saccharomyces cerevisiae and other eukaryotes. This includes a high degree of conservation for many fundamental classes of transcription factors, such as RNA polymerase II, general transcription factors, particular coactivators, chromatin remodeling complexes, and histone modification enzymes (6, 30). Other features are less well conserved, particularly the DNA regulatory sites that control transcription. While TATA elements are used at a significant number of promoters in both S. cerevisiae and metazoans, the TATA-start site distance is fixed in metazoans but not in S. cerevisiae, and the start site itself is more conserved in metazoans (68). In addition, downstream promoter elements, widely used in metazoans, are not found in S. cerevisiae (40).Another significant difference between yeast and metazoans concerns yeast upstream activation sequences (UASs) and their metazoan counterparts, enhancers. Both serve as binding sites for gene-specific activators, yet while UASs are usually positioned within a few hundred base pairs 5Ј of the TATA box or core promoter, enhancers are often located several kilobases away from or even 3Ј of the promoter (5, 30). While there is some evidence that yeast UASs cannot function when moved too far from their promoters (31, 71), this area has not been extensively studied. As the S. cerevisiae genome is compact, and the majority of yeast promoters range from approximately 150 to 400 bp (28, 59), it seems logical that there would be restrictions on activation distance in order to maintain specificity between a UAS and its target gene. However, there is no clear understanding of the effect of distance on activation in S.

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

Cited by 97 publications

References 71 publications

Genetic Analysis of the Human Papillomavirus Type 31 Differentiation-Dependent Late Promoter

Genetic Analysis of the Human Papillomavirus Type 31 Differentiation-Dependent Late Promoter

Enhancer Choice in Cis and in Trans in Drosophila melanogaster

Analysis of Transcriptional Activation at a Distance inSaccharomyces cerevisiae

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