Stability of transcription complexes on class II genes.

Dyke, Michael W. Van; Sawadogo, Michèle; Roeder, Robert G.

doi:10.1128/mcb.9.1.342

Cited by 99 publications

(69 citation statements)

References 14 publications

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“…The slopes of the curves with and without competitor (the two upper curves) are indistinguishable for 20 min, showing that the competitor has not substantially interrupted the process of continuous RNA production. This result is consistent with earlier template commitment experiments done with a different TATA-containing template that showed that once the template is transcribed it is preferentially retranscribed (12,35).…”

Section: Resultssupporting

confidence: 82%

“…For RNA polymerase II, different pathways were first suggested by in vitro studies that showed that a transcribed template appeared to be preferentially used through multiple rounds, in contrast to templates that have not been transcribed previously (12). The source of this preference was thought to be that TFIID remained bound to the template after initial polymerase escape and promoter clearance, thus facilitating formation of the new assemblies used for transcription reinitiation (12,35). Very recent studies confirm that TFIID can be left behind after initiation (27,41).…”

mentioning

confidence: 95%

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Transcription Reinitiation Rate: a Special Role for the TATA Box

Yean

Gralla

1997

Molecular and Cellular Biology

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Promoters need to specify both the timing of transcriptional induction and the amount of transcript synthesized. In order to explore each of these effects separately, in vitro assays for the level of active preinitiation complex formation and for the rate of continuous RNA production were done. The effects were found to be influenced differently by different promoter elements. A consensus TATA element had a very strong effect on the rate of continuous RNA production, whereas two types of activators were important primarily in forming active transcription preinitiation complexes. Consensus TATA promoters exhibited high rates of continuous transcription; they assembled active preinitiation transcription complexes slowly but then produced transcripts continuously at an approximately fivefold-higher rate. Initiator-containing TATA-less promoters produced continuous transcripts slowly. Point mutations in the TATA element led to lower levels of transcription by reducing the number of preinitiation complexes and amplifying this reduction by lowering the apparent reinitiation rate. The results allow understanding of the sequence diversity of promoter elements in terms of specifying separate controls over the sensitivity of gene induction and over the strength of the induced promoter.The DNA elements that comprise RNA polymerase II promoters should serve two functions. First, they need to specify under what circumstances transcription will be activated. Thus, they cause appropriate activation during development, physiological induction, or cell cycle progression. The primary means of activation is thought to be at the level of assembly of functional preinitiation complexes (for recent reviews, see references 11, 13 and 34). Second, the elements should specify the amount of transcript produced from the activated promoter. Once a gene is activated, the amount of its transcript is determined primarily by the number of transcription reinitiation events. Fully induced promoters can differ in the amount of RNA produced, indicating that promoter elements can influence promoter strength separately from how they influence induction. The potential separation of the roles of elements in stimulation of induction and in promoter strength has not been explored in depth.It has been suggested that the controls over RNA polymerase II initiation and reinitiation can be uncoupled (14), raising the possibility that the two processes can have different requirements. Related issues have been discussed for all three types of eukaryotic RNA polymerases (7,14,24). For initiation and reinitiation requirements to differ, the processes must use different pathways to produce transcripts, as is well known for RNA polymerase III (17). For RNA polymerase II, different pathways were first suggested by in vitro studies that showed that a transcribed template appeared to be preferentially used through multiple rounds, in contrast to templates that have not been transcribed previously (12). The source of this preference was thought to be that TFIID remaine...

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Section: Resultssupporting

confidence: 82%

mentioning

confidence: 95%

Transcription Reinitiation Rate: a Special Role for the TATA Box

Yean

Gralla

1997

Molecular and Cellular Biology

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“…This slower mobility of GFP-TBP is consistent with other kinetic studies demonstrating that TFIID dissociates from chromatin slowly (Burley, 1996). The significant difference in the rate of fluorescence recovery between GFP-TBP and GFP-TFIIB provides evidence in live cells, supporting that TFIID remains promoter-associated during transcription, whereas TFIIB dissociates during the transition from initiation to elongation (Van Dyke et al, 1988;Van Dyke et al, 1989;Zawel et al, 1995), and that TFIIB reassociates with TFIID, individually, to reform the RNA polymerase II docking site or as part of a holoenzyme (Zawel et al, 1995).Summarily, we have analyzed the dynamic behavior of TBP in live mammalian cells for the first time, using GFP-TBP and FRAP analyses. We have shown that TBP-TAF complexes involved in RNA polymerase II and III transcription are associated with transcriptionally silent mitotic chromatin.…”

supporting

confidence: 76%

TBP Dynamics in Living Human Cells: Constitutive Association of TBP with Mitotic Chromosomes

Chen¹,

Hinkley²,

Henry³

et al. 2002

MBoC

135

117

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The recruitment of TATA binding protein (TBP) to gene promoters is a critical rate-limiting step in transcriptional regulation for all three eukaryotic RNA polymerases. However, little is known regarding the dynamics of TBP in live mammalian cells. In this report, we examined the distribution and dynamic behavior of green fluorescence protein (GFP)-tagged TBP in live HeLa cells using fluorescence recovery after photobleaching (FRAP) analyses. We observed that GFP-TBP associates with condensed chromosomes throughout mitosis without any FRAP. These results suggest that TBP stably associates with the condensed chromosomes during mitosis. In addition, endogenous TBP and TBP-associated factors (TAFs), specific for RNA polymerase II and III transcription, cofractionated with mitotic chromatin, suggesting that TBP is retained as a TBP-TAF complex on transcriptionally silent chromatin throughout mitosis. In interphase cells, GFP-TBP distributes throughout the nucleoplasm and shows a FRAP that is 100-fold slower than the general transcription factor GFP-TFIIB. This difference supports the idea that TBP and, most likely, TBP-TAF complexes, remain promoter-bound for multiple rounds of transcription. Altogether, our observations demonstrate that there are cell cycle specific characteristics in the dynamic behavior of TBP. We propose a novel model in which the association of TBP-TAF complexes with chromatin during mitosis marks genes for rapid transcriptional activation as cells emerge from mitosis. INTRODUCTIONIn eukaryotic cells, the three RNA polymerases I, II, and III are dedicated to the transcription of distinct classes of genes. Distinct promoter architectures and the assembly of polymerase-specific initiation complexes at gene promoters are keys that dictate the recruitment of the particular class of polymerases. TATA binding protein (TBP) interacts with a variety of TBP-associated factors (TAFs) to form the selectivity factor-1 (SL1), transcription factor TFIID, and TFIIIB complexes that are important for specifying RNA polymerase I, II, and III transcription, respectively (Hernandez, 1993). TBP-TAF complexes are critical players in determining levels of transcription initiation. Thus, the formation of specific TBP-TAF complexes potentially regulates transcription of specific genes under different growth conditions. Increasing the recruitment of these complexes to gene promoters by regulatory proteins is one mechanism for transcriptional activation (Albright and Tjian, 2000;Hampsey and Reinberg, 1999;Hernandez, 1993;Lee and Young, 1998). Once recruited to a promoter, TBP-TAF complexes can perform additional functions that are important for transcriptional regulation, including recruitment of additional members of the general transcriptional machinery to the promoter, induction of conformational changes in DNA topology, and recruitment of coactivator or corepressor proteins that influence gene transcription (reviewed in Tansey and Herr, 1997).The various TBP-TAF complexes have been purified and characterized extensiv...

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“…Components of the general transcription machinery are functionally conserved among eukaryotes, as evidenced by the ability of TFIIA and TFIID from Saccharomyces cerevisiae to substitute for the corresponding HeLa factors in vitro (2,4,14,21). TFIID binding to the TATA element initiates the assembly of the other factors into a preinitiation complex (1,34,54,55). Yeast TFIID (yTFIID) and the TATA-binding subunit of TFIID (designated TFIIDT or TBP) from higher eukaryotes contain a highly conserved 180-amino-acid C-terminal domain and divergent N-terminal regions (3, 8, 11, 15-18, 22, 25, 33, 35, 47, 52).…”

mentioning

confidence: 99%

TFIIA induces conformational changes in TFIID via interactions with the basic repeat.

Lee¹,

DeJong²,

Hashimoto³

et al. 1992

Mol. Cell. Biol.

Self Cite

110

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. Components of the general transcription machinery are functionally conserved among eukaryotes, as evidenced by the ability of TFIIA and TFIID from Saccharomyces cerevisiae to substitute for the corresponding HeLa factors in vitro (2,4,14,21). TFIID binding to the TATA element initiates the assembly of the other factors into a preinitiation complex (1,34,54,55). Yeast TFIID (yTFIID) and the TATA-binding subunit of TFIID (designated TFIIDT or TBP) from higher eukaryotes contain a highly conserved 180-amino-acid C-terminal domain and divergent N-terminal regions (3, 8, 11, 15-18, 22, 25, 33, 35, 47, 52). Biochemical and genetic studies have shown that the conserved C-terminal domain of TFIID'T contains all of the essential regions for DNA binding, transcription initiation, and species specificity (6,13,23,36,40,56,57). TFIID shows unusual binding properties compared with those of the other sequence-specific DNA binding proteins: e.g., a temperature dependency and slow on and off rates (20,28,48).The binding of TFIID to DNA can be stimulated by TFIIA, apparently by direct interactions of TFIIA with TFIID (1, 30). The ability of TFIIA to interact directly with TFIID has allowed efficient purification of this protein from both HeLa cells (7, 7a, 53) and S. cerevisiae (38). TFIIA has been shown to function at an early step in the formation of a preinitiation complex (10,41). In contrast to the absolute requirement for the other transcription factors, a consistent requirement for TFIIA in the initiation of transcription has not been observed (for a review, see reference 42). This may reflect the nature of the TFIID-employed cross-contamination of factors, the presence of alternative factors, or the * Corresponding author. particular conditions of transcription (1, 7, 31, 32, 41-45, 51, 55). For example, the transcription factor TFIIG initially was identified as a factor which substitutes for TFIIA in basal transcription and which further stimulates TFIIAsaturated transcription (51). The initiator-binding transcription factor TFII-I (43) has been shown to substitute for TFIIA in transcription of the adenovirus major late (AdML) core promoter, suggesting alternative pathways for the formation of preinitiation complexes, possibly with different rates of formation and/or complex stabilities (for a review, see reference 42; 42a). The function(s) of TFIIA in preinitiation complex formation and transcription initiation has yet to be elucidated.Interactions of negative cofactors which bind competitively with TFIIA to TFIID on DNA have also been reported elsewhere (31,32). These negative cofactors dissociate TFIIA or TFIIB from the intermediary preinitiation complexes to produce nonproductive preinitiation complexes (negative cofactor-TFIID-DNA complexes) that result in repressed promoter states (for a review, see reference 42). Preincubation of promoters with TFIIA and native TFIID was shown to increase basal levels of transcription with corresponding decreases in promoter stimulation by activators, suggesting the involvem...

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Stability of transcription complexes on class II genes.

Cited by 99 publications

References 14 publications

Transcription Reinitiation Rate: a Special Role for the TATA Box

Transcription Reinitiation Rate: a Special Role for the TATA Box

TBP Dynamics in Living Human Cells: Constitutive Association of TBP with Mitotic Chromosomes

TFIIA induces conformational changes in TFIID via interactions with the basic repeat.

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