Changing the RNA polymerase specificity of U snRNA gene promoters

Mattaj, Iain W.; Dathan, Nina A.; Parry, Huw D.; Carbon, Philippe; Krol, Alain

doi:10.1016/0092-8674(88)90029-3

Cited by 162 publications

(169 citation statements)

References 29 publications

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“…PSE swapping experiments between U2 and U6 genes have demonstrated that different PSEs are functionally interchangeable and per se are not responsible for polymerase selection (25,28,35). It is likely, therefore, that the transcription factor(s) bound to the PSE elements directly interacts with both class II and class III transcription factors to assist in RNA polymerase selection.…”

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“…Like their class II snRNA gene counterparts, class III snRNA genes have similar DSE and PSE configurations but additionally contain a TATA-like sequence at position Ϫ25. The TATA box of class III snRNA genes is required for efficient transcription and functions as the major determinant of RNA Pol III specificity (25,28).The PSE sequence is found almost exclusively in the promoters of snRNA genes and is the only common essential promoter element through which both classes of snRNA genes can be coordinately regulated. PSE swapping experiments between U2 and U6 genes have demonstrated that different PSEs are functionally interchangeable and per se are not responsible for polymerase selection (25,28,35).…”

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confidence: 99%

“…The TATA box of class III snRNA genes is required for efficient transcription and functions as the major determinant of RNA Pol III specificity (25,28).…”

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Proximal Sequence Element-Binding Transcription Factor (PTF) Is a Multisubunit Complex Required for Transcription of both RNA Polymerase II- and RNA Polymerase III-Dependent Small Nuclear RNA Genes

Yoon

Murphy

Bai

et al. 1995

Molecular and Cellular Biology

120

131

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The proximal sequence element (PSE), found in both RNA polymerase II (Pol II)-and RNA Pol IIItranscribed small nuclear RNA (snRNA) genes, is specifically bound by the PSE-binding transcription factor (PTF). We have purified PTF to near homogeneity from HeLa cell extracts by using a combination of conventional and affinity chromatographic methods. Purified PTF is composed of four polypeptides with apparent molecular masses of 180, 55, 45, and 44 kDa. A combination of preparative electrophoretic mobility shift and sodium dodecyl sulfate-polyacrylamide gel electrophoresis analyses has conclusively identified these four polypeptides as subunits of human PTF, while UV cross-linking experiments demonstrate that the largest subunit of PTF is in close contact with the PSE. The purified PTF activates transcription from promoters of both Pol II-and Pol III-transcribed snRNA genes in a PSE-dependent manner. In addition, we have investigated factor requirements in transcription of Pol III-dependent snRNA genes. We show that in extracts that have been depleted of TATA-binding protein (TBP) and associated factors, recombinant TBP restores transcription from U6 and 7SK promoters but not from the VAI promoter, whereas the highly purified TBP-TBPassociated factor complex TFIIIB restores transcription from the VAI but not the U6 or 7SK promoter. Furthermore, by complementation of heat-treated extracts lacking TFIIIC activity, we show that TFIIIC1 is required for transcription of both the 7SK and VAI genes, whereas TFIIIC2 is required only for transcription of the VAI gene. From these observations, we conclude (i) that PTF and TFIIIC2 function as gene-specific factors for PSE-and B-box-containing Pol III genes, respectively, (ii) that the form of TBP used by class III genes with upstream promoter elements differs from the form used by class III genes with internal promoters, and (iii) that TFIIIC1 is required for both internal and external Pol III promoters.Mammalian small nuclear RNA (snRNA) genes contain related promoter structures, but some (class II) are transcribed by RNA polymerase II (Pol II), whereas others (class III) are transcribed by RNA Pol III (reviewed in references 8, 15, 23, 30, and 37). Class II snRNA genes (e.g., U1 to U5) contain two regulatory elements in the 5Ј-flanking region: a distal sequence element (DSE) located approximately 220 bp upstream of the transcription start site, and a proximal sequence element (PSE) centered around Ϫ55. The DSE contains at least one copy of the octamer motif and functions as an upstream enhancer, whereas the PSE is an essential promoter element which functions in start site selection and may be required for accurate 3Ј-end formation (17,33,35). The promoters of class III snRNA genes (e.g., 7SK and U6) are located solely in the 5Ј-flanking region and lack intragenic control elements typical of most other class III genes (9, 29). Like their class II snRNA gene counterparts, class III snRNA genes have similar DSE and PSE configurations but additionally contain a TATA-like sequen...

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“…The TATA box of class III snRNA genes is required for efficient transcription and functions as the major determinant of RNA Pol III specificity (25,28).…”

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Proximal Sequence Element-Binding Transcription Factor (PTF) Is a Multisubunit Complex Required for Transcription of both RNA Polymerase II- and RNA Polymerase III-Dependent Small Nuclear RNA Genes

Yoon

Murphy

Bai

et al. 1995

Molecular and Cellular Biology

120

131

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“…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). All, however, have regulatory sequences which more closely resemble polymerase II than polymerase III promoters: they are entirely upstream of the transcribed gene, have TATA boxes at approximately -30, and use a common upstream activator protein, Oct 1, which also affects polymerase II protein gene promoters (20,22,28,31,51,52). Most surprisingly, simple changes in spacing between the promoter elements could change the RNA polymerase which expressed the snRNA (18,52).…”

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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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The U6 gene of Saccharomyces cerevisiae is transcribed by RNA polymerase C (III) in vivo and in vitro.

et al. 1990

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Unlike the majority of genes encoding small nuclear RNAs, which are transcribed by RNA polymerase B, the U6 gene contains features found in both class B and class C genes, indicating the involvement of a combination of transcription factors normally specific to each class of genes. We present direct genetic and biochemical evidence that the U6 gene of Saccharomyces cerevisiae is transcribed by RNA polymerase C in vivo as well as in vitro. A mutant strain with a temperature‐sensitive defect in the large subunit of RNA polymerase C that results in defective transcription of tRNA and 5S RNA genes shows a corresponding defect in U6 RNA levels. Also, purified RNA polymerase C transcribes the U6 gene when supplemented with partially purified TFIIIB. The other class C transcription factors, TFIIIA and Tau (TFIIIC), are not required in this system.

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Changing the RNA polymerase specificity of U snRNA gene promoters

Cited by 162 publications

References 29 publications

Proximal Sequence Element-Binding Transcription Factor (PTF) Is a Multisubunit Complex Required for Transcription of both RNA Polymerase II- and RNA Polymerase III-Dependent Small Nuclear RNA Genes

Proximal Sequence Element-Binding Transcription Factor (PTF) Is a Multisubunit Complex Required for Transcription of both RNA Polymerase II- and RNA Polymerase III-Dependent Small Nuclear RNA Genes

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.

The U6 gene of Saccharomyces cerevisiae is transcribed by RNA polymerase C (III) in vivo and in vitro.

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