Participation of the TATA Factor in Transcription of the Yeast U6 Gene by RNA Polymerase C

Margottin, Florence; Dujardin, Geneviève; Gérard, Matthieu; Egly, Jean‐Marc; Huet, Janine; Sentenac, André

doi:10.1126/science.1989075

Cited by 177 publications

(127 citation statements)

References 32 publications

(25 reference statements)

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“…In the polymerase II and III systems, binding to antibody or to promoter DNA might be mutually exclusive, resulting in complete dissociation of the complex at high antibody titers. In opposition to this notion, we (26,30), although polymerases I and III have more subunits in common (9,45 (Fig. 3).…”

Section: Discussionmentioning

confidence: 81%

“…Most surprisingly, simple changes in spacing between the promoter elements could change the RNA polymerase which expressed the snRNA (18,52). These observations prompted Margottin et al (26) to test the yeast RNA polymerase II transcription factor which binds to the TATA sequence element (now known as TFIIDr or TBP) for function in U6 snRNA transcription. TBP was found to be required for yeast U6 transcription by polymerase III and later by the cognate HeLa U6 RNA transcription system (23,46).…”

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confidence: 99%

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TATA box-binding protein (TBP) is a constituent of the polymerase I-specific transcription initiation factor TIF-IB (SL1) bound to the rRNA promoter and shows differential sensitivity to TBP-directed reagents in polymerase I, II, and III transcription factors.

Radebaugh¹,

Matthews²,

Geiss³

et al. 1994

Mol. Cell. Biol.

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The role of the Acanthamoeba casteUlanii TATA-binding protein (TBP) in transcription was examined. Specific antibodies against the nonconserved N-terminal domain of TBP were used to verify the presence of TBP in the fundamental transcription initiation factor for RNA polymerase I, TIF-IB, and to demonstrate that TBP is part of the committed initiation complex on the rRNA promoter. The same antibodies inhibit transcription in all three polymerase systems, but they do so differentially. Oligonucleotide competitors were used to evaluate the accessibility of the TATA-binding site in TIF-IB, TFIID, and TFIIIB. The results suggest that insertion of TBP into the polymerase II and III factors is more similar than insertion into the polymerase I factor.While the transcription systems of eukaryotic RNA polymerases I, II, and III obviously share some characteristics, initiation mechanisms for these transcription systems have been largely studied separately. The polymerases themselves have five subunits in common, seven in the case of the "odd pols," RNA polymerases I and III (45). Nevertheless, the general transcription factors involved with each polymerase have been examined in isolation, perhaps masking important generalizations about their functions. This approach began to change when it was discovered that some of the genes for small nuclear RNAs (snRNAs) are transcribed by polymerase III whereas most are transcribed by polymerase II (27,32,35,47 The full impact of this factor overlap was perhaps not realized because polymerase I still appeared to use dedicated factors. However, a flurry of studies (6,7,44,56) revealed that TBP was required for transcription of all genes. TBP is now known to be a subunit of TFIID (41), TFIIIB (17,24,48,55), and human TIF-IB (SL1) (6). TBP is associated with additional subunits (TAFs) to make up the functional factors (reviewed in reference 41). The TAFs appear to be different for each polymerase system (reviewed in reference 42), although overlap of TAFs has not been rigorously ruled out. All the TBP-containing factors are pivotal for their respective polymerases. Indeed, TFIIIB and TIF-IB are fundamental transcription factors; i.e., they appear to be responsible for the repetitive recruitment of RNA polymerase during successive rounds of initiation (16; reviewed in references 36 and 37).The manner by which the TBP-containing factor is recruited to the promoter differs from gene to gene. For RNA polymerase III genes with type I (SS RNA) or type II (tRNA, VAI, Alu, EBER, 7SL, 4.5S) internal control regions, additional general transcription factors are required to assemble TFIIIB onto the promoter (reviewed in references 10-12). Initiation complex formation on 5S and tRNA genes is an organized process in which the factors bind in an obligatory order, each relying on protein-DNA and protein-protein interactions with a previously bound factor(s) to join the complex. On some genes the DNA interaction site for TFIIIB is sequence specific, whereas on others specific sequence recognition is no...

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Section: Discussionmentioning

confidence: 81%

mentioning

confidence: 99%

TATA box-binding protein (TBP) is a constituent of the polymerase I-specific transcription initiation factor TIF-IB (SL1) bound to the rRNA promoter and shows differential sensitivity to TBP-directed reagents in polymerase I, II, and III transcription factors.

Radebaugh¹,

Matthews²,

Geiss³

et al. 1994

Mol. Cell. Biol.

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“…Seifart and colleagues published in 1988 the partial purification of human TFIIIB. 17 After the molecular cloning of the TATA-binding protein (TBP) from human cells 18,19 and the discovery that TBP participates in U6 transcription in yeast 20 and human cells [21][22][23] it became clear that it is also involved in the transcription of RNAP III genes with internal promoter elements. 24 Subsequently, TBP and associated factors were purified that reconstituted TFIIIB activity at gene internal promoters.…”

Section: Tfiiiamentioning

confidence: 99%

Contributions of in vitro transcription to the understanding of human RNA polymerase III transcription

et al. 2014

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The discovery of constituents of eukaryotic transcription systems was enabled by the development of in vivo and in vitro methods for their study. Depending on the organism to be studied, the relative importance of each of these two general approaches has been different. Our knowledge about transcription of human genes would be considerably smaller without the results that were obtained by employing in vitro methods. Here, we will mainly focus on in vitro studies of gene expression that contributed to discoveries in the human RNA polymerase (RNAP) III transcription system.In contrast to unicellular yeast, it has until today been and will most likely remain for a many more years impossible to study human RNAP III transcription in cells that have been grown under conditions resembling at least approximately to an in vivo situation in a human being. For that reason, it has hitherto been difficult to address questions concerning the physiological regulation of human RNAP III transcription in its natural environment. However, the identification of the basal components of the RNAP III transcription system could be achieved without directly resorting to a human "in vivo model system." Yet, the identification of human RNAP III subunits and of accessory transcription factors repeatedly took advantage of in vivo systems that were established in other species. Many discoveries of components of the human RNAP III transcription system were fostered by work performed in unicellular (for example, S. cerevisiae and S. pombe) and multicellular eukaryotes (among others, X. laevis or D. melanogaster). Often, results obtained in these model systems helped researchers identify proteins of the human RNAP III transcription system. For instance, the amino acid sequences of transcription factors that were identified and cloned by employing in vivo and in vitro methods in these organisms served as guide for comparing and identifying orthologous transcription factors in human cells (e.g., TFIIIA, TFIIIB [BDP1], TFIIIC35 [GTF3C6]). However, several of the human RNAP III transcription factors were not cloned by homology, but due to extensive purification from human cells (TFIIIB [BRF2], PTF/SNAPc, TFIIIC [GTF3C1-5]). Purification of these factors by employing biochemical methods was only possible, because functional assays were developed that allowed detecting their specific activities. These assays included in vitro transcription, electrophoretic mobility shift assays (EMSA) and footprinting techniques (descriptions of these techniques are found in 1-3 ). Two techniques were essential for the biochemical purification and functional analysis of human transcription factors: (i) the elaboration of protocols that allowed deriving protein extracts from human cells and (ii) the development of cell-free in vitro transcription assays. [4][5][6] Template DNA for in vitro transcription was provided by genes cloned into plasmid DNA. In the case of RNAP III transcription, usually complete and generally short transcribed sequences were included into the...

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“…Two sets of observations show that TFIIIB is the central initiation factor of pol III: 1) TFIIIC can be removed from tRNA genes after TFIIIB is assembled at the promoter without loss of transcription activity (13). 2) SNR6, which does not require TFIIIC for loading TFIIIB in vitro, can be transcribed by pol III in the presence of TFIIIB only (15,16); TFIIIB components have been demonstrated to contact pol III subunits directly (17)(18)(19)(20)(21).…”

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The Brf and TATA-binding Protein Subunits of the RNA Polymerase III Transcription Factor IIIB Mediate Position-specific Integration of the Gypsy-like Element, Ty3

Yieh

Kassavetis

Geiduschek

et al. 2000

Journal of Biological Chemistry

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Ty3 integrates into the transcription initiation sites of genes transcribed by RNA polymerase III. It is known that transcription factors (TF) IIIB and IIIC are important for recruiting Ty3 to its sites of integration upstream of tRNA genes, but that RNA polymerase III is not required. In order to investigate the respective roles of TFIIIB and TFIIIC, we have developed an in vitro integration assay in which Ty3 is targeted to the U6 small nuclear RNA gene, SNR6. Because TFIIIB can bind to the TATA box upstream of the U6 gene through contacts mediated by TATA-binding protein (TBP), TFIIIC is dispensable for in vitro transcription. Thus, this system offers an opportunity to test the role of TFIIIB independent of a requirement of TFIIIC. We demonstrate that the recombinant Brf and TBP subunits of TFIIIB, which interact over the SNR6 TATA box, direct integration at the SNR6 transcription initiation site in the absence of detectable TFIIIC or TFIIIB subunit B؆. These findings suggest that the minimal requirements for pol III transcription and Ty3 integration are very similar.Integration site selection is a key step in the retroelement life cycle, potentially influencing both the effect of the insertion on the host genome and the expression of the element itself. Similar to retroviruses, yeast Ty elements transpose through reverse transcription of an almost full-length RNA copy into a full-length DNA copy, which is integrated into the host genome. Despite very similar molecular mechanisms of integration, budding yeast elements (Tys), both gypsy-like (Ty3) and copialike (Ty1, 2, 4, and 5), differ from retroviruses in that they exhibit dramatic global integration site preferences (1-4). Ty1 elements, for example, integrate preferentially within a window of 750 bp, 1 upstream of genes transcribed by RNA polymerase III (pol III). Analysis of the yeast genome sequence shows that Ty2 and Ty4 also occupy this region upstream of a fraction of tRNA genes. Ty5 integrates into regions of silenced DNA, including the silent mating type loci and telomeres. Hence Ty1, Ty2, Ty4, and Ty5 exhibit regional integration specificity. Despite similarities with these other elements, Ty3 differs in that it integrates within a highly defined window, one or two base pairs (bp) upstream of pol III transcription initiation sites.Targeting of integration appears to be directed by the cooperative actions of Ty3 element-and cell-encoded factors. For example, in addition to the element-encoded integrase protein, Ty3 and Ty1 targeting requires the presence of a transcriptionally competent pol III promoter (5, 6), and Ty5 targeting requires factors involved in the establishment of silent chromatin (7).Class III genes, including plasmid-borne U6, 5S, and tRNA genes, are used in vivo for position-specific Ty3 integration. Comparison of integration sites suggests that Ty3 integration preference is not a direct function of specific local sequences. Each class of pol III-transcribed genes differs from the others in composition of promoter elements (8) and d...

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Participation of the TATA Factor in Transcription of the Yeast U6 Gene by RNA Polymerase C

Cited by 177 publications

References 32 publications

TATA box-binding protein (TBP) is a constituent of the polymerase I-specific transcription initiation factor TIF-IB (SL1) bound to the rRNA promoter and shows differential sensitivity to TBP-directed reagents in polymerase I, II, and III transcription factors.

TATA box-binding protein (TBP) is a constituent of the polymerase I-specific transcription initiation factor TIF-IB (SL1) bound to the rRNA promoter and shows differential sensitivity to TBP-directed reagents in polymerase I, II, and III transcription factors.

Contributions of in vitro transcription to the understanding of human RNA polymerase III transcription

The Brf and TATA-binding Protein Subunits of the RNA Polymerase III Transcription Factor IIIB Mediate Position-specific Integration of the Gypsy-like Element, Ty3

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