Skip to main content
PMC home page
The EMBO Journal logoLink to The EMBO Journal
. 1997 Jun 15;16(12):3633–3643. doi: 10.1093/emboj/16.12.3633

Transcriptional termination signals for RNA polymerase II in fission yeast.

C E Birse 1, B A Lee 1, K Hansen 1, N J Proudfoot 1
PMCID: PMC1169987  PMID: 9218804

Abstract

Transcription 'run-on' (TRO) analysis using permeabilized yeast cells indicates that transcription terminates between 180 and 380 bp downstream of the poly(A) site of the Schizosaccharomyces pombe ura4 gene. Two signals direct RNA polymerase II (pol II) to stop transcription: the previously identified 3' end formation signals located close to the poly(A) site and an additional downstream element (DSE) located at the region of termination. The downstream signal (135 bp) appears to act by pausing the elongating polymerase. TRO analysis indicates that elevated levels of transcribing polymerases accumulate over the DSE and that removal of this signal leads to transcription proceeding beyond the normal termination region. Furthermore, when inserted between two competing polyadenylation signals, this DSE increases the utilization of upstream poly(A) sites in vivo. We show that polymerase pausing over an extended region of template ensures termination of pol II transcription close to the poly(A) site.

Full Text

The Full Text of this article is available as a PDF (459.2 KB).

Selected References

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

  1. Akhtar A., Faye G., Bentley D. L. Distinct activated and non-activated RNA polymerase II complexes in yeast. EMBO J. 1996 Sep 2;15(17):4654–4664. [PMC free article] [PubMed] [Google Scholar]
  2. Allison D. S., Hall B. D. Effects of alterations in the 3' flanking sequence on in vivo and in vitro expression of the yeast SUP4-o tRNATyr gene. EMBO J. 1985 Oct;4(10):2657–2664. doi: 10.1002/j.1460-2075.1985.tb03984.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Connelly S., Manley J. L. A CCAAT box sequence in the adenovirus major late promoter functions as part of an RNA polymerase II termination signal. Cell. 1989 May 19;57(4):561–571. doi: 10.1016/0092-8674(89)90126-8. [DOI] [PubMed] [Google Scholar]
  4. Connelly S., Manley J. L. A functional mRNA polyadenylation signal is required for transcription termination by RNA polymerase II. Genes Dev. 1988 Apr;2(4):440–452. doi: 10.1101/gad.2.4.440. [DOI] [PubMed] [Google Scholar]
  5. Connelly S., Manley J. L. RNA polymerase II transcription termination is mediated specifically by protein binding to a CCAAT box sequence. Mol Cell Biol. 1989 Nov;9(11):5254–5259. doi: 10.1128/mcb.9.11.5254. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. Edwalds-Gilbert G., Prescott J., Falck-Pedersen E. 3' RNA processing efficiency plays a primary role in generating termination-competent RNA polymerase II elongation complexes. Mol Cell Biol. 1993 Jun;13(6):3472–3480. doi: 10.1128/mcb.13.6.3472. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. Eggermont J., Proudfoot N. J. Poly(A) signals and transcriptional pause sites combine to prevent interference between RNA polymerase II promoters. EMBO J. 1993 Jun;12(6):2539–2548. doi: 10.1002/j.1460-2075.1993.tb05909.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Enriquez-Harris P., Levitt N., Briggs D., Proudfoot N. J. A pause site for RNA polymerase II is associated with termination of transcription. EMBO J. 1991 Jul;10(7):1833–1842. doi: 10.1002/j.1460-2075.1991.tb07709.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. Humphrey T., Birse C. E., Proudfoot N. J. RNA 3' end signals of the S.pombe ura4 gene comprise a site determining and efficiency element. EMBO J. 1994 May 15;13(10):2441–2451. doi: 10.1002/j.1460-2075.1994.tb06529.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. Humphrey T., Sadhale P., Platt T., Proudfoot N. Homologous mRNA 3' end formation in fission and budding yeast. EMBO J. 1991 Nov;10(11):3503–3511. doi: 10.1002/j.1460-2075.1991.tb04914.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. Hyman L. E., Moore C. L. Termination and pausing of RNA polymerase II downstream of yeast polyadenylation sites. Mol Cell Biol. 1993 Sep;13(9):5159–5167. doi: 10.1128/mcb.13.9.5159. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. Hyman L. E., Seiler S. H., Whoriskey J., Moore C. L. Point mutations upstream of the yeast ADH2 poly(A) site significantly reduce the efficiency of 3'-end formation. Mol Cell Biol. 1991 Apr;11(4):2004–2012. doi: 10.1128/mcb.11.4.2004. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. James P., Hall B. D. ret1-1, a yeast mutant affecting transcription termination by RNA polymerase III. Genetics. 1990 Jun;125(2):293–303. doi: 10.1093/genetics/125.2.293. [DOI] [PMC free article] [PubMed] [Google Scholar]
  14. James P., Whelen S., Hall B. D. The RET1 gene of yeast encodes the second-largest subunit of RNA polymerase III. Structural analysis of the wild-type and ret1-1 mutant alleles. J Biol Chem. 1991 Mar 25;266(9):5616–5624. [PubMed] [Google Scholar]
  15. Jerome J. F., Jaehning J. A. mRNA transcription in nuclei isolated from Saccharomyces cerevisiae. Mol Cell Biol. 1986 May;6(5):1633–1639. doi: 10.1128/mcb.6.5.1633. [DOI] [PMC free article] [PubMed] [Google Scholar]
  16. Köhrer K., Domdey H. Preparation of high molecular weight RNA. Methods Enzymol. 1991;194:398–405. doi: 10.1016/0076-6879(91)94030-g. [DOI] [PubMed] [Google Scholar]
  17. Lang W. H., Morrow B. E., Ju Q., Warner J. R., Reeder R. H. A model for transcription termination by RNA polymerase I. Cell. 1994 Nov 4;79(3):527–534. doi: 10.1016/0092-8674(94)90261-5. [DOI] [PubMed] [Google Scholar]
  18. Lanoix J., Acheson N. H. A rabbit beta-globin polyadenylation signal directs efficient termination of transcription of polyomavirus DNA. EMBO J. 1988 Aug;7(8):2515–2522. doi: 10.1002/j.1460-2075.1988.tb03099.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  19. Logan J., Falck-Pedersen E., Darnell J. E., Jr, Shenk T. A poly(A) addition site and a downstream termination region are required for efficient cessation of transcription by RNA polymerase II in the mouse beta maj-globin gene. Proc Natl Acad Sci U S A. 1987 Dec;84(23):8306–8310. doi: 10.1073/pnas.84.23.8306. [DOI] [PMC free article] [PubMed] [Google Scholar]
  20. Maundrell K. nmt1 of fission yeast. A highly transcribed gene completely repressed by thiamine. J Biol Chem. 1990 Jul 5;265(19):10857–10864. [PubMed] [Google Scholar]
  21. Osborne B. I., Guarente L. Mutational analysis of a yeast transcriptional terminator. Proc Natl Acad Sci U S A. 1989 Jun;86(11):4097–4101. doi: 10.1073/pnas.86.11.4097. [DOI] [PMC free article] [PubMed] [Google Scholar]
  22. Pribyl T. M., Martinson H. G. Transcription termination at the chicken beta H-globin gene. Mol Cell Biol. 1988 Dec;8(12):5369–5377. doi: 10.1128/mcb.8.12.5369. [DOI] [PMC free article] [PubMed] [Google Scholar]
  23. Rocco V., de Massy B., Nicolas A. The Saccharomyces cerevisiae ARG4 initiator of meiotic gene conversion and its associated double-strand DNA breaks can be inhibited by transcriptional interference. Proc Natl Acad Sci U S A. 1992 Dec 15;89(24):12068–12072. doi: 10.1073/pnas.89.24.12068. [DOI] [PMC free article] [PubMed] [Google Scholar]
  24. Rougvie A. E., Lis J. T. The RNA polymerase II molecule at the 5' end of the uninduced hsp70 gene of D. melanogaster is transcriptionally engaged. Cell. 1988 Sep 9;54(6):795–804. doi: 10.1016/s0092-8674(88)91087-2. [DOI] [PubMed] [Google Scholar]
  25. Ruohola H., Baker S. M., Parker R., Platt T. Orientation-dependent function of a short CYC1 DNA fragment in directing mRNA 3' end formation in yeast. Proc Natl Acad Sci U S A. 1988 Jul;85(14):5041–5045. doi: 10.1073/pnas.85.14.5041. [DOI] [PMC free article] [PubMed] [Google Scholar]
  26. Snyder M., Sapolsky R. J., Davis R. W. Transcription interferes with elements important for chromosome maintenance in Saccharomyces cerevisiae. Mol Cell Biol. 1988 May;8(5):2184–2194. doi: 10.1128/mcb.8.5.2184. [DOI] [PMC free article] [PubMed] [Google Scholar]
  27. Strobl L. J., Eick D. Hold back of RNA polymerase II at the transcription start site mediates down-regulation of c-myc in vivo. EMBO J. 1992 Sep;11(9):3307–3314. doi: 10.1002/j.1460-2075.1992.tb05409.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  28. Tantravahi J., Alvira M., Falck-Pedersen E. Characterization of the mouse beta maj globin transcription termination region: a spacing sequence is required between the poly(A) signal sequence and multiple downstream termination elements. Mol Cell Biol. 1993 Jan;13(1):578–587. doi: 10.1128/mcb.13.1.578. [DOI] [PMC free article] [PubMed] [Google Scholar]
  29. Whitelaw E., Proudfoot N. Alpha-thalassaemia caused by a poly(A) site mutation reveals that transcriptional termination is linked to 3' end processing in the human alpha 2 globin gene. EMBO J. 1986 Nov;5(11):2915–2922. doi: 10.1002/j.1460-2075.1986.tb04587.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  30. Zaret K. S., Sherman F. DNA sequence required for efficient transcription termination in yeast. Cell. 1982 Mar;28(3):563–573. doi: 10.1016/0092-8674(82)90211-2. [DOI] [PubMed] [Google Scholar]

Articles from The EMBO Journal are provided here courtesy of Nature Publishing Group

RESOURCES