scholarly journals The proximal sequence element (PSE) plays a major role in establishing the RNA polymerase specificity of Drosophila U-snRNA genes

1998 ◽  
Vol 26 (2) ◽  
pp. 616-622 ◽  
Author(s):  
R. C. Jensen ◽  
Y. Wang ◽  
S. B. Hardin ◽  
W. E. Stumph
Keyword(s):  
Rna Polymerase ◽  
Sequence Element ◽  
Proximal Sequence Element

scholarly journals 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.

1995 ◽  
Vol 15 (4) ◽  
pp. 2019-2027 ◽  
Author(s):  
J B Yoon ◽  
S Murphy ◽  
L Bai ◽  
Z Wang ◽  
R G Roeder
Keyword(s):  
Rna Polymerase ◽  
Rna Polymerase Ii ◽  
Small Nuclear Rna ◽  
Class Iii ◽  
Sequence Element ◽  
Pol Ii ◽  
Proximal Sequence Element ◽  
Nuclear Rna ◽  
Class Iii Genes ◽  
Pol Iii

The proximal sequence element (PSE), found in both RNA polymerase II (Pol II)- and RNA Pol III-transcribed 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-TBP-associated 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 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 from used by class III genes with internal promoters, and (iii) that TFIIIC1 is required for both internal and external Pol III promoters.

Oct-1 and Oct-2 potentiate functional interactions of a transcription factor with the proximal sequence element of small nuclear RNA genes

1992 ◽  
Vol 12 (7) ◽  
pp. 3247-3261
Author(s):  
S Murphy ◽  
J B Yoon ◽  
T Gerster ◽  
R G Roeder
Keyword(s):  
Transcription Factor ◽  
Rna Polymerase ◽  
Rna Polymerase Ii ◽  
Rna Polymerase Iii ◽  
Small Nuclear Rna ◽  
Sequence Element ◽  
Proximal Sequence Element ◽  
Pou Domain ◽  
Polymerase Iii ◽  
Nuclear Rna

The promoters of both RNA polymerase II- and RNA polymerase III-transcribed small nuclear RNA (snRNA) genes contain an essential and highly conserved proximal sequence element (PSE) approximately 55 bp upstream from the transcription start site. In addition, the upstream enhancers of all snRNA genes contain binding sites for octamer-binding transcription factors (Octs), and functional studies have indicated that the PSE and octamer elements work cooperatively. The present study has identified and characterized a novel transcription factor (designated PTF) which specifically binds to the PSE sequence of both RNA polymerase II- and RNA polymerase III-transcribed snRNA genes. PTF binding is markedly potentiated by Oct binding to an adjacent octamer site. This potentiation is effected by Oct-1, Oct-2, or the conserved POU domain of these factors. In agreement with these results and despite the independent binding of Octs to the promoter, PTF and Oct-1 enhance transcription from the 7SK promoter in an interdependent manner. Moreover, the POU domain of Oct-1 is sufficient for significant in vitro activity in the presence of PTF. These results suggest that essential activation domains reside in PTF and that the potentiation of PTF binding by Octs plays a key role in the function of octamer-containing snRNA gene enhancers.

scholarly journals Architectural Arrangement of Cloned Proximal Sequence Element-Binding Protein Subunits on Drosophila U1 and U6 snRNA Gene Promoters

2004 ◽  
Vol 24 (5) ◽  
pp. 1897-1906 ◽  
Author(s):  
Cheng Li ◽  
Gale A. Harding ◽  
Jason Parise ◽  
Kathleen J. McNamara-Schroeder ◽  
William E. Stumph
Keyword(s):  
Rna Polymerase ◽  
Rna Polymerase Ii ◽  
Binding Protein ◽  
Rna Polymerase Iii ◽  
Cross Linking ◽  
Gene Promoters ◽  
Sequence Element ◽  
Proximal Sequence Element ◽  
U6 Snrna ◽  
Cloned Gene

ABSTRACT Transcription of snRNA genes by either RNA polymerase II (U1 to U5) or RNA polymerase III (U6) is dependent upon a proximal sequence element (PSE) located approximately 40 to 60 bp upstream of the transcription start site. In Drosophila melanogaster, RNA polymerase specificity is determined by as few as three nucleotide differences within the otherwise well-conserved 21-bp PSE. Previous photo-cross-linking studies revealed that the D. melanogaster PSE-binding protein, DmPBP, contains three subunits (DmPBP45, DmPBP49, and DmPBP95) that associate with the DNA to form complexes that are conformationally distinct depending upon whether the protein is bound to a U1 or a U6 PSE. We have identified and cloned the genes that code for these subunits of DmPBP by virtue of their similarity to three of the five subunits of SNAPc, the human PBP. When expressed in S2 cells, each of the three cloned gene products is incorporated into a protein complex that functionally binds to a PSE. We also find that the conformational difference referred to above is particularly pronounced for DmPBP45, herein identified as the ortholog of human SNAP43. DmPBP45 cross-linked strongly to DNA for two turns of the DNA helix downstream of the U1 PSE, but it cross-linked strongly for only a half turn of the helix downstream of a U6 PSE. These substantial differences in the cross-linking pattern are consistent with those of a model in which conformational differences in DmPBP-DNA complexes lead to selective RNA polymerase recruitment to U1 and U6 promoters.

scholarly journals Identification and Topological Arrangement ofDrosophila Proximal Sequence Element (PSE)-Binding Protein Subunits That Contact the PSEs of U1 and U6 Small Nuclear RNA Genes

1998 ◽  
Vol 18 (3) ◽  
pp. 1570-1579 ◽  
Author(s):  
Yan Wang ◽  
William E. Stumph
Keyword(s):  
Rna Polymerase ◽  
Rna Polymerase Ii ◽  
Sea Urchins ◽  
Binding Protein ◽  
Rna Polymerase Iii ◽  
Specific Protein ◽  
Cross Linking ◽  
Sequence Element ◽  
Proximal Sequence Element ◽  
U6 Gene

ABSTRACT Most small nuclear RNAs (snRNAs) are synthesized by RNA polymerase II, but U6 and a few others are synthesized by RNA polymerase III. Transcription of snRNA genes by either polymerase is dependent on a proximal sequence element (PSE) located upstream of position −40 relative to the transcription start site. In contrast to findings in vertebrates, sea urchins, and plants, the RNA polymerase specificity ofDrosophila snRNA genes is intrinsically encoded in the PSE sequence itself. We have investigated the differential interaction of the Drosophila melanogaster PSE-binding protein (DmPBP) with U1 and U6 gene PSEs. By using a site specific protein-DNA photo-cross-linking assay, we identified three polypeptide subunits of DmPBP with apparent molecular masses of 95, 49, and 45 kDa that are in close proximity to the DNA and two additional putative polypeptides of 230 and 52 kDa that may be integral to the complex. The 95-kDa subunit cross-linked at positions spanning the entire length of the PSE, but the 49- and 45-kDa subunits cross-linked only to the 3′ half of the PSE. The same polypeptides cross-linked to both the U1 and U6 PSE sequences. However, there were significant differences in the cross-linking patterns of these subunits at a subset of the phosphate positions, depending on whether binding was to a U1 or U6 gene PSE. These data suggest that RNA polymerase specificity is associated with distinct modes of interaction of DmPBP with the DNA at U1 and U6 promoters.

scholarly journals Oct-1 and Oct-2 potentiate functional interactions of a transcription factor with the proximal sequence element of small nuclear RNA genes.

1992 ◽  
Vol 12 (7) ◽  
pp. 3247-3261 ◽  
Author(s):  
S Murphy ◽  
J B Yoon ◽  
T Gerster ◽  
R G Roeder
Keyword(s):  
Transcription Factor ◽  
Rna Polymerase ◽  
Rna Polymerase Ii ◽  
Rna Polymerase Iii ◽  
Small Nuclear Rna ◽  
Sequence Element ◽  
Proximal Sequence Element ◽  
Pou Domain ◽  
Polymerase Iii ◽  
Nuclear Rna

The promoters of both RNA polymerase II- and RNA polymerase III-transcribed small nuclear RNA (snRNA) genes contain an essential and highly conserved proximal sequence element (PSE) approximately 55 bp upstream from the transcription start site. In addition, the upstream enhancers of all snRNA genes contain binding sites for octamer-binding transcription factors (Octs), and functional studies have indicated that the PSE and octamer elements work cooperatively. The present study has identified and characterized a novel transcription factor (designated PTF) which specifically binds to the PSE sequence of both RNA polymerase II- and RNA polymerase III-transcribed snRNA genes. PTF binding is markedly potentiated by Oct binding to an adjacent octamer site. This potentiation is effected by Oct-1, Oct-2, or the conserved POU domain of these factors. In agreement with these results and despite the independent binding of Octs to the promoter, PTF and Oct-1 enhance transcription from the 7SK promoter in an interdependent manner. Moreover, the POU domain of Oct-1 is sufficient for significant in vitro activity in the presence of PTF. These results suggest that essential activation domains reside in PTF and that the potentiation of PTF binding by Octs plays a key role in the function of octamer-containing snRNA gene enhancers.

scholarly journals Cloning and characterization of the beta subunit of human proximal sequence element-binding transcription factor and its involvement in transcription of small nuclear RNA genes by RNA polymerases II and III.

1996 ◽  
Vol 16 (10) ◽  
pp. 5419-5426 ◽  
Author(s):  
L Bai ◽  
Z Wang ◽  
J B Yoon ◽  
R G Roeder
Keyword(s):  
Transcription Factor ◽  
Rna Polymerase ◽  
Rna Polymerase Ii ◽  
Rna Polymerase Iii ◽  
Small Nuclear Rna ◽  
Class Iii ◽  
Sequence Element ◽  
Proximal Sequence Element ◽  
Nuclear Rna

The proximal sequence element (PSE)-binding transcription factor (PTF), which binds the PSE of both RNA polymerase II- and RNA polymerase III-transcribed mammalian small nuclear RNA (snRNA) genes, is essential for their transcription. We previously reported the purification of human PTF, a complex of four subunits, and the molecular cloning and characterization of PTF gamma and delta subunits. Here we describe the isolation and expression of a cDNA encoding PTF beta, as well as functional studies using anti-PTF beta antibodies. Native PTF beta, in either protein fractions or a PTF-Oct-1-DNA complex, can be recognized by polyclonal antibodies raised against recombinant PTF beta. Immunodepletion studies show that PTF beta is required for transcription of both classes of snRNA genes in vitro. In addition, immunoprecipitation analyses demonstrate that substantial and similar molar amounts of TATA-binding protein (TBP) and TFIIIB90 can weakly associate with PTF at low salt conditions, but this association is dramatically reduced at high salt concentrations. Along with our previous demonstration of both physical interactions between PTF gamma/PTF delta and TBP and the involvement of TFIIIB90 in the transcription of class III snRNA genes, these results are consistent with the notion that a TBP-containing complex related to TFIIIB is required for the transcription of class III snRNA genes, and acts through weak interaction with the four-subunit PTF.

scholarly journals Cloning of two proximal sequence element-binding transcription factor subunits (gamma and delta) that are required for transcription of small nuclear RNA genes by RNA polymerases II and III and interact with the TATA-binding protein.

1996 ◽  
Vol 16 (1) ◽  
pp. 1-9 ◽  
Author(s):  
J B Yoon ◽  
R G Roeder
Keyword(s):  
Transcription Factor ◽  
Rna Polymerase ◽  
Binding Protein ◽  
Rna Polymerase Iii ◽  
Class Ii ◽  
Tata Binding Protein ◽  
Small Nuclear Rna ◽  
Sequence Element ◽  
Proximal Sequence Element ◽  
Nuclear Rna

The proximal sequence element (PSE)-binding transcription factor (PTF) specifically recognizes the PSEs of both RNA polymerase II- and RNA polymerase III-transcribed small nuclear RNA (snRNA) genes. We previously have shown that PTF purified from human HeLa cells is a multisubunit complex of four polypeptides designated PTF alpha, -beta, -gamma, and -delta. We now report the isolation and expression of cDNAs encoding PTF gamma and PTF delta, as well as functional studies with cognate antibodies that recognize the native PTF complex in HeLa extracts. Immunoprecipitation studies confirm that the four PTF subunits originally found to copurify during conventional chromatography indeed form a tightly associated complex; they further show that the PTF so defined, including the gamma and delta subunits specifically, is essential for transcription of both class II and class III snRNA genes. Immunoprecipitation assays also show a weak substoichiometric association of the TATA-binding protein (TBP) with PTF, consistent with the previous report of a PTF-related complex (SNAPc) containing substoichiometric levels of TBP and a component (SNAPc43) identical in sequence to the PTF gamma reported here. Glutathione S-transferase pulldown assays further indicate relatively strong direct interactions of both recombinant PTF gamma and PTF delta with TBP, consistent either with the natural association of TBP with PTF in a semistable TBP-TBP-associated factor complex or with possible functional interactions between PSE-bound PTF and TATA-bound TBP during promoter activation. In addition, we show that in extracts depleted of TBP and TBP-associated factors, transcription from the U1 promoter is restored by recombinant TBP but not by TFIID or TFIIIB, indicating that transcription of class II snRNA genes requires a TBP complex different from the one used for mRNA-encoding genes.

Transcription initiation from the dihydrofolate reductase promoter is positioned by HIP1 binding at the initiation site

1990 ◽  
Vol 10 (2) ◽  
pp. 653-661
Author(s):  
A L Means ◽  
P J Farnham
Keyword(s):  
Rna Polymerase ◽  
Binding Site ◽  
Rna Polymerase Ii ◽  
Dihydrofolate Reductase ◽  
Transcription Initiation ◽  
Simian Virus 40 ◽  
Initiation Site ◽  
Simian Virus ◽  
Sequence Element ◽  
Initiator Element

We have identified a sequence element that specifies the position of transcription initiation for the dihydrofolate reductase gene. Unlike the functionally analogous TATA box that directs RNA polymerase II to initiate transcription 30 nucleotides downstream, the positioning element of the dihydrofolate reductase promoter is located directly at the site of transcription initiation. By using DNase I footprint analysis, we have shown that a protein binds to this initiator element. Transcription initiated at the dihydrofolate reductase initiator element when 28 nucleotides were inserted between it and all other upstream sequences, or when it was placed on either side of the DNA helix, suggesting that there is no strict spatial requirement between the initiator and an upstream element. Although neither a single Sp1-binding site nor a single initiator element was sufficient for transcriptional activity, the combination of one Sp1-binding site and the dihydrofolate reductase initiator element cloned into a plasmid vector resulted in transcription starting at the initiator element. We have also shown that the simian virus 40 late major initiation site has striking sequence homology to the dihydrofolate reductase initiation site and that the same, or a similar, protein binds to both sites. Examination of the sequences at other RNA polymerase II initiation sites suggests that we have identified an element that is important in the transcription of other housekeeping genes. We have thus named the protein that binds to the initiator element HIP1 (Housekeeping Initiator Protein 1).

scholarly journals A nucleosome positioned in the distal promoter region activates transcription of the human U6 gene.

1997 ◽  
Vol 17 (8) ◽  
pp. 4397-4405 ◽  
Author(s):  
W Stünkel ◽  
I Kober ◽  
K H Seifart
Keyword(s):  
Micrococcal Nuclease ◽  
Deletion Mutants ◽  
Dna Fragments ◽  
Wild Type ◽  
Sequence Element ◽  
Proximal Sequence Element ◽  
Experimental Approaches ◽  
Type Gene ◽  
Distal Promoter ◽  
U6 Gene

To investigate the consequences of chromatin reconstitution for transcription of the human U6 gene, we assembled nucleosomes on both plasmids and linear DNA fragments containing the U6 gene. Initial experiments with DNA fragments revealed that U6 sequences located between the distal sequence element (DSE) and the proximal sequence element (PSE) lead to the positioning of a nucleosome partially encompassing these promoter elements. Furthermore, indirect end-labelling analyses of the reconstituted U6 wild-type plasmids showed strong micrococcal nuclease cuts near the DSE and PSE, indicating that a nucleosome is located between these elements. To investigate the influence that nucleosomes exert on U6 transcription, we used two different experimental approaches for chromatin reconstitution, both of which resulted in the observation that transcription of the U6 wild-type gene was enhanced after chromatin assembly. To ensure that the facilitated transcription of the nucleosomal templates is in fact due to a positioned nucleosome, we constructed mutants of the U6 gene in which the sequences between the DSE and PSE were progressively deleted. In contrast to what was observed with the wild-type genes, transcription of these deletion mutants was significantly inhibited when they were packaged into nucleosomes.

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