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. 1998 Jan 15;26(2):616–622. doi: 10.1093/nar/26.2.616

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

R C Jensen 1, Y Wang 1, S B Hardin 1, W E Stumph 1
PMCID: PMC147272  PMID: 9421524

Abstract

Most small nuclear RNA (snRNA) genes are transcribed by RNA polymerase II, but some (e.g., U6) are transcribed by RNA polymerase III. In vertebrates a TATA box at a fixed distance downstream of the proximal sequence element (PSE) acts as a dominant determinant for recruiting RNA polymerase III to U6 gene promoters. In contrast, vertebrate snRNA genes that contain a PSE but lack a TATA box are transcribed by RNA polymerase II. In plants, transcription of both classes of snRNA genes requires a TATA box in addition to an upstream sequence element (USE), and polymerase specificity is determined by the spacing between these two core promoter elements. In these examples, the PSE (or USE) is interchangeable between the two classes of snRNA genes. Here we report the surprising finding that the Drosophila U1 and U6 PSEs cannot functionally substitute for each other; rather, determination of RNA polymerase specificity is an intrinsic property of the PSE sequence itself. The alteration of two or three base pairs near the 3'-end of the U1 and U6 PSEs was sufficient to switch the RNA polymerase specificity of Drosophila snRNA promoters in vitro. These findings reveal a novel mechanism for achieving RNA polymerase specificity at insect snRNA promoters.

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Selected References

These references are in PubMed. This may not be the complete list of references from this article.

  1. Dahlberg J. E., Lund E. How does III x II make U6? Science. 1991 Dec 6;254(5037):1462–1463. doi: 10.1126/science.1962205. [DOI] [PubMed] [Google Scholar]
  2. Das G., Henning D., Reddy R. Structure, organization, and transcription of Drosophila U6 small nuclear RNA genes. J Biol Chem. 1987 Jan 25;262(3):1187–1193. [PubMed] [Google Scholar]
  3. Goomer R. S., Kunkel G. R. The transcriptional start site for a human U6 small nuclear RNA gene is dictated by a compound promoter element consisting of the PSE and the TATA box. Nucleic Acids Res. 1992 Sep 25;20(18):4903–4912. doi: 10.1093/nar/20.18.4903. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. Kiss T., Marshallsay C., Filipowicz W. Alteration of the RNA polymerase specificity of U3 snRNA genes during evolution and in vitro. Cell. 1991 May 3;65(3):517–526. doi: 10.1016/0092-8674(91)90469-f. [DOI] [PubMed] [Google Scholar]
  5. Lescure A., Carbon P., Krol A. The different positioning of the proximal sequence element in the Xenopus RNA polymerase II and III snRNA promoters is a key determinant which confers RNA polymerase III specificity. Nucleic Acids Res. 1991 Feb 11;19(3):435–441. doi: 10.1093/nar/19.3.435. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. Li J. M., Haberman R. P., Marzluff W. F. Common factors direct transcription through the proximal sequence elements (PSEs) of the embryonic sea urchin U1, U2, and U6 genes despite minimal similarity among the PSEs. Mol Cell Biol. 1996 Mar;16(3):1275–1281. doi: 10.1128/mcb.16.3.1275. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. Li J. M., Parsons R. A., Marzluff W. F. Transcription of the sea urchin U6 gene in vitro requires a TATA-like box, a proximal sequence element, and sea urchin USF, which binds an essential E box. Mol Cell Biol. 1994 Mar;14(3):2191–2200. doi: 10.1128/mcb.14.3.2191. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Lo P. C., Mount S. M. Drosophila melanogaster genes for U1 snRNA variants and their expression during development. Nucleic Acids Res. 1990 Dec 11;18(23):6971–6979. doi: 10.1093/nar/18.23.6971. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. Lobo S. M., Hernandez N. A 7 bp mutation converts a human RNA polymerase II snRNA promoter into an RNA polymerase III promoter. Cell. 1989 Jul 14;58(1):55–67. doi: 10.1016/0092-8674(89)90402-9. [DOI] [PubMed] [Google Scholar]
  10. Lobo S. M., Lister J., Sullivan M. L., Hernandez N. The cloned RNA polymerase II transcription factor IID selects RNA polymerase III to transcribe the human U6 gene in vitro. Genes Dev. 1991 Aug;5(8):1477–1489. doi: 10.1101/gad.5.8.1477. [DOI] [PubMed] [Google Scholar]
  11. Mattaj I. W., Dathan N. A., Parry H. D., Carbon P., Krol A. Changing the RNA polymerase specificity of U snRNA gene promoters. Cell. 1988 Nov 4;55(3):435–442. doi: 10.1016/0092-8674(88)90029-3. [DOI] [PubMed] [Google Scholar]
  12. Parry H. D., Tebb G., Mattaj I. W. The Xenopus U2 gene PSE is a single, compact, element required for transcription initiation and 3' end formation. Nucleic Acids Res. 1989 May 25;17(10):3633–3644. doi: 10.1093/nar/17.10.3633. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. Stefanovic B., Marzluff W. F. Characterization of two developmentally regulated sea urchin U2 small nuclear RNA promoters: a common required TATA sequence and independent proximal and distal elements. Mol Cell Biol. 1992 Feb;12(2):650–660. doi: 10.1128/mcb.12.2.650. [DOI] [PMC free article] [PubMed] [Google Scholar]
  14. Steinberg T. H., Mathews D. E., Durbin R. D., Burgess R. R. Tagetitoxin: a new inhibitor of eukaryotic transcription by RNA polymerase III. J Biol Chem. 1990 Jan 5;265(1):499–505. [PubMed] [Google Scholar]
  15. Vankan P., Filipowicz W. A U-snRNA gene-specific upstream element and a -30 'TATA box' are required for transcription of the U2 snRNA gene of Arabidopsis thaliana. EMBO J. 1989 Dec 1;8(12):3875–3882. doi: 10.1002/j.1460-2075.1989.tb08566.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  16. Waibel F., Filipowicz W. RNA-polymerase specificity of transcription of Arabidopsis U snRNA genes determined by promoter element spacing. Nature. 1990 Jul 12;346(6280):199–202. doi: 10.1038/346199a0. [DOI] [PubMed] [Google Scholar]
  17. Waibel F., Filipowicz W. U6 snRNA genes of Arabidopsis are transcribed by RNA polymerase III but contain the same two upstream promoter elements as RNA polymerase II-transcribed U-snRNA genes. Nucleic Acids Res. 1990 Jun 25;18(12):3451–3458. doi: 10.1093/nar/18.12.3451. [DOI] [PMC free article] [PubMed] [Google Scholar]
  18. Wang Y., Jensen R. C., Stumph W. E. Role of TATA box sequence and orientation in determining RNA polymerase II/III transcription specificity. Nucleic Acids Res. 1996 Aug 1;24(15):3100–3106. doi: 10.1093/nar/24.15.3100. [DOI] [PMC free article] [PubMed] [Google Scholar]
  19. Wang Y., Stumph W. E. RNA polymerase II/III transcription specificity determined by TATA box orientation. Proc Natl Acad Sci U S A. 1995 Sep 12;92(19):8606–8610. doi: 10.1073/pnas.92.19.8606. [DOI] [PMC free article] [PubMed] [Google Scholar]
  20. Wendelburg B. J., Marzluff W. F. Two promoter elements are necessary and sufficient for expression of the sea urchin U1 snRNA gene. Nucleic Acids Res. 1992 Jul 25;20(14):3743–3751. doi: 10.1093/nar/20.14.3743. [DOI] [PMC free article] [PubMed] [Google Scholar]
  21. Zamrod Z., Tyree C. M., Song Y., Stumph W. E. In vitro transcription of a Drosophila U1 small nuclear RNA gene requires TATA box-binding protein and two proximal cis-acting elements with stringent spacing requirements. Mol Cell Biol. 1993 Sep;13(9):5918–5927. doi: 10.1128/mcb.13.9.5918. [DOI] [PMC free article] [PubMed] [Google Scholar]

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