TBP-DNA interactions in the minor groove discriminate between A:T and T:A base pairs

Wong, Jiemin; Bateman, Erik

doi:10.1093/nar/22.10.1890

Cited by 74 publications

(60 citation statements)

References 35 publications

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“…All EMSA experiments were done using wild-type and T3-flip probes that contained SNR6 sequence from Ϫ45 to Ϫ8, which was found to be the minimal sequence required to assemble a TFIIIB-DNA complex (5). Binding of TBP might be affected by the T3-flip mutation, since in vitro analysis of TBP binding demonstrates a preference for specific sequences flanking the TATA box (24,45). However, TBP exhibited no marked preference for binding wild-type or mutant probes (Fig.…”

Section: Resultsmentioning

confidence: 99%

A Novel Upstream RNA Polymerase III Promoter Element Becomes Essential When the Chromatin Structure of the Yeast U6 RNA Gene Is Altered

Martin

Gerlach

Brow

2001

Molecular and Cellular Biology

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The Saccharomyces cerevisiae U6 RNA gene, SNR6, possesses upstream sequences that allow productive binding in vitro of the RNA polymerase III (Pol III) transcription initiation factor IIIB (TFIIIB) in the absence of TFIIIC or other assembly factors. TFIIIC-independent transcription of SNR6 in vitro is highly sensitive to point mutations in a consensus TATA box at position ؊30. In contrast, the TATA box is dispensable for SNR6 transcription in vivo, apparently because TFIIIC bound to the intragenic A block and downstream B block can recruit TFIIIB via protein-protein interactions. A mutant allele of SNR6 with decreased spacing between the A and B blocks, snr6-⌬42, exhibits increased dependence on the upstream sequences in vivo. Unexpectedly, we find that in vivo expression of snr6-⌬42 is much more sensitive to mutations in a (dT-dA) 7 tract between the TATA box and transcription start site than to mutations in the TATA box itself. Inversion of single base pairs in the center of the dT-dA tract nearly abolishes transcription of snr6-⌬42, yet inversion of all 7 base pairs has little effect on expression, indicating that the dA-dT tract is relatively orientation independent. Although it is within the TFIIIB footprint, point mutations in the dT-dA tract do not inhibit TFIIIB binding or TFIIICindependent transcription of SNR6 in vitro. In the absence of the chromatin architectural protein Nhp6, dT-dA tract mutations are lethal even when A-to-B block spacing is wild type. We conclude that the (dT-dA) 7 tract and Nhp6 cooperate to direct productive transcription complex assembly on SNR6 in vivo.Initiation of transcription by an RNA polymerase at the start site of a gene involves multiple protein-DNA interactions, but one protein-DNA interaction often has a dominant role in specifying the site and efficiency of transcription complex assembly. For example, a central step in initiation by eukaryotic RNA polymerase II (Pol II) on many protein-coding genes is binding of transcription factor (TF) IID, via its TATA-binding protein (TBP) subunit, to an upstream TATA box promoter element. A key step in initiation by Pol III on tRNA genes is binding of TFIIIC to two intragenic promoter elements, the A and B blocks. TFIIIC then places TFIIIB upstream of the transcription start site (reviewed in reference 9). These distinct promoter recognition steps in Pol II and Pol III transcription imply divergent mechanisms for initiation complex assembly. Yet further characterization of Pol II and Pol III transcription initiation complexes has revealed striking similarities. For example, like TFIID, TFIIIB contains the TATA-binding protein as a subunit. Although most Pol III transcription units lack a consensus TATA box in the TFIIIB-binding region, A/T-rich sequences 15 to 30 base pairs upstream of the start site are known to contribute to the efficiency of tRNA and 5S rRNA gene transcription in vitro (29, 38) and in vivo (23,40). In addition, an increasing number of Pol II transcription units have been found to contain TFIID-binding promote...

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Section: Resultsmentioning

confidence: 99%

A Novel Upstream RNA Polymerase III Promoter Element Becomes Essential When the Chromatin Structure of the Yeast U6 RNA Gene Is Altered

Martin

Gerlach

Brow

2001

Molecular and Cellular Biology

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“…Heterogeneity in the location of bound TBP would account both for the longer protected region and for the fuzziness of the footprint boundaries. Inspection of all of the 7-bp sequences within the TBP footprint revealed three candidates, based on TBP binding preferences inferred from Pol II transcription (57) or direct binding measurements (45,58 . We considered the other 7-bp segments unlikely because they contain either C or A in the first position or A in the third position, and these departures from a canonical TATA are known to reduce TBP binding (45).…”

Section: Resultsmentioning

confidence: 99%

TATA-Binding Protein–TATA Interaction Is a Key Determinant of Differential Transcription of Silkworm Constitutive and Silk Gland-Specific tRNA^Ala Genes

Ouyang

Martinez

Young

et al. 2000

Molecular and Cellular Biology

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We have investigated the contribution of specific TATA-binding protein (TBP)-TATA interactions to the promoter activity of a constitutively expressed silkworm tRNA C Ala gene and have also asked whether the lack of similar interactions accounts for the low promoter activity of a silk gland-specific tRNA SG Ala gene. We compared TBP binding, TFIIIB-promoter complex stability (measured by heparin resistance), and in vitro transcriptional activity in a series of mutant tRNA C Ala promoters and found that specific TBP-TATA contacts are important for TFIIIB-promoter interaction and for transcriptional activity. Although the wild-type tRNA C Ala promoter contains two functional TBP binding sequences that overlap, the tRNA SG Ala promoter lacks any TBP binding site in the corresponding region. This feature appears to account for the inefficiency of the tRNA SG Ala promoter since provision of either of the wild-type TATA sequences derived from the tRNA C Ala promoter confers robust transcriptional activity. Transcriptional impairment of the wild-type tRNA SG Ala gene is not due to reduced incorporation of TBP into transcription complexes since both the tRNA C Ala and tRNA SG Ala promoters form transcription complexes that contain the same amount of TBP. Thus, the deleterious consequences of the lack of appropriate TBP-TATA contacts in the tRNA SG Ala promoter must come from failure to incorporate some other essential transcription factor(s) or to stabilize the complete complex in an active conformation.The silkworm Bombyx mori provides a clear example of regulated tRNA gene expression. The demand for fibroin, the principal protein of silk, requires highly efficient transcription and translation of the fibroin gene in cells of the silk gland. Translational efficiency in these cells is maximized by the quantitative adaptation of the tRNA population to the composition of fibroin: 44% glycine, 29% alanine, and 12% serine (5,29,30,42). In the case of tRNA Ala , enrichment is achieved both by increasing the level of the constitutive type of tRNA Ala (tRNA C Ala ) and by synthesizing an additional, silk gland-specific, type (tRNA SG Ala ) (31,44). In vitro studies of representative tRNA C Ala and tRNA SG Ala genes have revealed transcription properties consistent with the patterns of tRNA C Ala and tRNA SG Ala accumulation in vivo. That is, in a variety of extracts from non-silk gland cells, the tRNA C Ala gene directs transcription much more efficiently than does the tRNA SG Ala gene, but in concentrated extracts from silk gland, the two genes are equally efficient (60). To understand how these two genes are differentially regulated, we have investigated the basis of the transcriptional impairment of the tRNA SG Ala gene that is observed under typical in vitro conditions. Transcription of silkworm tRNA Ala genes is driven by both internal and external promoter elements (26,36,56). The critical difference between the tRNA C Ala and tRNA SG Ala genes is in the interaction of their 5Ј flanking promoter elements with the transcri...

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“…Despite the marked preference for A:T and T:A base pairs, C:G and/or G:C base pairs occur frequently at five of the eight positions. Thus, TBP can bind productively to a large number of diverse TATA elements, some of which bear little resemblance to the optimal TATA sequence (5Ј-TATATAAG-3Ј), identified by an in vitro binding-site selection experiment with Acanthamoeba TBP (Wong and Bateman 1994).…”

mentioning

confidence: 99%

TATA element recognition by the TATA box-binding protein has been conserved throughout evolution

Patikoglou¹,

Kim²,

Sun³

et al. 1999

Genes & Development

277

331

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TBP-DNA interactions in the minor groove discriminate between A:T and T:A base pairs

Cited by 74 publications

References 35 publications

A Novel Upstream RNA Polymerase III Promoter Element Becomes Essential When the Chromatin Structure of the Yeast U6 RNA Gene Is Altered

A Novel Upstream RNA Polymerase III Promoter Element Becomes Essential When the Chromatin Structure of the Yeast U6 RNA Gene Is Altered

TATA-Binding Protein–TATA Interaction Is a Key Determinant of Differential Transcription of Silkworm Constitutive and Silk Gland-Specific tRNA^Ala Genes

TATA element recognition by the TATA box-binding protein has been conserved throughout evolution

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TBP-DNA interactions in the minor groove discriminate between A:T and T:A base pairs

Cited by 74 publications

References 35 publications

A Novel Upstream RNA Polymerase III Promoter Element Becomes Essential When the Chromatin Structure of the Yeast U6 RNA Gene Is Altered

A Novel Upstream RNA Polymerase III Promoter Element Becomes Essential When the Chromatin Structure of the Yeast U6 RNA Gene Is Altered

TATA-Binding Protein–TATA Interaction Is a Key Determinant of Differential Transcription of Silkworm Constitutive and Silk Gland-Specific tRNAAla Genes

TATA element recognition by the TATA box-binding protein has been conserved throughout evolution

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TATA-Binding Protein–TATA Interaction Is a Key Determinant of Differential Transcription of Silkworm Constitutive and Silk Gland-Specific tRNA^Ala Genes