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. 1998 Mar;4(3):303–318.

Transcription termination downstream of the Saccharomyces cerevisiae FBP1 [changed from FPB1] poly(A) site does not depend on efficient 3'end processing.

A Aranda 1, J E Pérez-Ortín 1, C Moore 1, M L del Olmo 1
PMCID: PMC1369619  PMID: 9510332

Abstract

Efficient transcription termination downstream of poly(A) sites has been shown to correlate with the strength of an upstream polyadenylation signal and the presence of a polymerase pause site. To further investigate the mechanism linking termination with 3'-end processing, we analyzed the cis-acting elements that contribute to these events in the Saccharomyces cerevisiae FBP1 gene. FBP1 has a complex polyadenylation signal, and at least three efficiency elements must be present for efficient processing. However, not all combinations of these elements are equally effective. This gene also shows a novel organization of sequence elements. A strong positioning element is located upstream, rather than downstream, of the efficiency elements, and functions to select the cleavage site in vitro and in vivo. Transcription run-on analysis indicated that termination occurs within 61 nt past the poly(A) site. Deletion of two UAUAUA-type efficiency elements greatly reduces polyadenylation in vivo and in vitro, but transcription termination is still efficient, implying that FBP1 termination signals may be distinct from those for polyadenylation. Alternatively, assembly of a partial, but nonfunctional, polyadenylation complex on the nascent transcript may be sufficient to cause termination.

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Selected References

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

  1. Aranda A., Pérez-Ortín J. E., Benham C. J., Del Olmo M. L. Analysis of the structure of a natural alternating d(TA)n sequence in yeast chromatin. Yeast. 1997 Mar 30;13(4):313–326. doi: 10.1002/(SICI)1097-0061(19970330)13:4<313::AID-YEA93>3.0.CO;2-8. [DOI] [PubMed] [Google Scholar]
  2. Ashfield R., Patel A. J., Bossone S. A., Brown H., Campbell R. D., Marcu K. B., Proudfoot N. J. MAZ-dependent termination between closely spaced human complement genes. EMBO J. 1994 Dec 1;13(23):5656–5667. doi: 10.1002/j.1460-2075.1994.tb06904.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Aviv H., Leder P. Purification of biologically active globin messenger RNA by chromatography on oligothymidylic acid-cellulose. Proc Natl Acad Sci U S A. 1972 Jun;69(6):1408–1412. doi: 10.1073/pnas.69.6.1408. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. Beelman C. A., Parker R. Degradation of mRNA in eukaryotes. Cell. 1995 Apr 21;81(2):179–183. doi: 10.1016/0092-8674(95)90326-7. [DOI] [PubMed] [Google Scholar]
  5. Birse C. E., Lee B. A., Hansen K., Proudfoot N. J. Transcriptional termination signals for RNA polymerase II in fission yeast. EMBO J. 1997 Jun 16;16(12):3633–3643. doi: 10.1093/emboj/16.12.3633. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. Brambilla A., Mainieri D., Agostoni Carbone M. L. A simple signal element mediates transcription termination and mRNA 3' end formation in the DEG1 gene of Saccharomyces cerevisiae. Mol Gen Genet. 1997 May;254(6):681–688. doi: 10.1007/s004380050466. [DOI] [PubMed] [Google Scholar]
  7. Butler J. S., Platt T. RNA processing generates the mature 3' end of yeast CYC1 messenger RNA in vitro. Science. 1988 Dec 2;242(4883):1270–1274. doi: 10.1126/science.2848317. [DOI] [PubMed] [Google Scholar]
  8. Chen J., Moore C. Separation of factors required for cleavage and polyadenylation of yeast pre-mRNA. Mol Cell Biol. 1992 Aug;12(8):3470–3481. doi: 10.1128/mcb.12.8.3470. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. Chen S., Reger R., Miller C., Hyman L. E. Transcriptional terminators of RNA polymerase II are associated with yeast replication origins. Nucleic Acids Res. 1996 Aug 1;24(15):2885–2893. doi: 10.1093/nar/24.15.2885. [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. Dammann R., Lucchini R., Koller T., Sogo J. M. Chromatin structures and transcription of rDNA in yeast Saccharomyces cerevisiae. Nucleic Acids Res. 1993 May 25;21(10):2331–2338. doi: 10.1093/nar/21.10.2331. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. Devereux J., Haeberli P., Smithies O. A comprehensive set of sequence analysis programs for the VAX. Nucleic Acids Res. 1984 Jan 11;12(1 Pt 1):387–395. doi: 10.1093/nar/12.1part1.387. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. Dujon B. The yeast genome project: what did we learn? Trends Genet. 1996 Jul;12(7):263–270. doi: 10.1016/0168-9525(96)10027-5. [DOI] [PubMed] [Google Scholar]
  13. 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]
  14. 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]
  15. Egli C. M., Springer C., Braus G. H. A complex unidirectional signal element mediates GCN4 mRNA 3' end formation in Saccharomyces cerevisiae. Mol Cell Biol. 1995 May;15(5):2466–2473. doi: 10.1128/mcb.15.5.2466. [DOI] [PMC free article] [PubMed] [Google Scholar]
  16. Elion E. A., Warner J. R. An RNA polymerase I enhancer in Saccharomyces cerevisiae. Mol Cell Biol. 1986 Jun;6(6):2089–2097. doi: 10.1128/mcb.6.6.2089. [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. 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]
  18. Funayama S., Gancedo J. M., Gancedo C. Turnover of yeast fructose-bisphosphatase in different metabolic conditions. Eur J Biochem. 1980 Aug;109(1):61–66. doi: 10.1111/j.1432-1033.1980.tb04767.x. [DOI] [PubMed] [Google Scholar]
  19. Gancedo J. M., Gancedo C. Fructose-1,6-diphosphatase, phosphofructokinase and glucose-6-phosphate dehydrogenase from fermenting and non fermenting yeasts. Arch Mikrobiol. 1971;76(2):132–138. doi: 10.1007/BF00411787. [DOI] [PubMed] [Google Scholar]
  20. Guo Z., Russo P., Yun D. F., Butler J. S., Sherman F. Redundant 3' end-forming signals for the yeast CYC1 mRNA. Proc Natl Acad Sci U S A. 1995 May 9;92(10):4211–4214. doi: 10.1073/pnas.92.10.4211. [DOI] [PMC free article] [PubMed] [Google Scholar]
  21. Guo Z., Sherman F. 3'-end-forming signals of yeast mRNA. Mol Cell Biol. 1995 Nov;15(11):5983–5990. doi: 10.1128/mcb.15.11.5983. [DOI] [PMC free article] [PubMed] [Google Scholar]
  22. Guo Z., Sherman F. 3'-end-forming signals of yeast mRNA. Trends Biochem Sci. 1996 Dec;21(12):477–481. doi: 10.1016/s0968-0004(96)10057-8. [DOI] [PubMed] [Google Scholar]
  23. Hegemann J. H., Fleig U. N. The centromere of budding yeast. Bioessays. 1993 Jul;15(7):451–460. doi: 10.1002/bies.950150704. [DOI] [PubMed] [Google Scholar]
  24. Heidmann S., Obermaier B., Vogel K., Domdey H. Identification of pre-mRNA polyadenylation sites in Saccharomyces cerevisiae. Mol Cell Biol. 1992 Sep;12(9):4215–4229. doi: 10.1128/mcb.12.9.4215. [DOI] [PMC free article] [PubMed] [Google Scholar]
  25. Henikoff S. Unidirectional digestion with exonuclease III creates targeted breakpoints for DNA sequencing. Gene. 1984 Jun;28(3):351–359. doi: 10.1016/0378-1119(84)90153-7. [DOI] [PubMed] [Google Scholar]
  26. Henry M., Borland C. Z., Bossie M., Silver P. A. Potential RNA binding proteins in Saccharomyces cerevisiae identified as suppressors of temperature-sensitive mutations in NPL3. Genetics. 1996 Jan;142(1):103–115. doi: 10.1093/genetics/142.1.103. [DOI] [PMC free article] [PubMed] [Google Scholar]
  27. 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]
  28. 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]
  29. Irniger S., Braus G. H. Saturation mutagenesis of a polyadenylation signal reveals a hexanucleotide element essential for mRNA 3' end formation in Saccharomyces cerevisiae. Proc Natl Acad Sci U S A. 1994 Jan 4;91(1):257–261. doi: 10.1073/pnas.91.1.257. [DOI] [PMC free article] [PubMed] [Google Scholar]
  30. Irniger S., Egli C. M., Braus G. H. Different classes of polyadenylation sites in the yeast Saccharomyces cerevisiae. Mol Cell Biol. 1991 Jun;11(6):3060–3069. doi: 10.1128/mcb.11.6.3060. [DOI] [PMC free article] [PubMed] [Google Scholar]
  31. Irniger S., Sanfaçon H., Egli C. M., Braus G. H. Different sequence elements are required for function of the cauliflower mosaic virus polyadenylation site in Saccharomyces cerevisiae compared with in plants. Mol Cell Biol. 1992 May;12(5):2322–2330. doi: 10.1128/mcb.12.5.2322. [DOI] [PMC free article] [PubMed] [Google Scholar]
  32. Ito H., Fukuda Y., Murata K., Kimura A. Transformation of intact yeast cells treated with alkali cations. J Bacteriol. 1983 Jan;153(1):163–168. doi: 10.1128/jb.153.1.163-168.1983. [DOI] [PMC free article] [PubMed] [Google Scholar]
  33. Kessler M. M., Zhao J., Moore C. L. Purification of the Saccharomyces cerevisiae cleavage/polyadenylation factor I. Separation into two components that are required for both cleavage and polyadenylation of mRNA 3' ends. J Biol Chem. 1996 Oct 25;271(43):27167–27175. doi: 10.1074/jbc.271.43.27167. [DOI] [PubMed] [Google Scholar]
  34. Kessler M. M., Zhelkovsky A. M., Skvorak A., Moore C. L. Monoclonal antibodies to yeast poly(A) polymerase (PAP) provide evidence for association of PAP with cleavage factor I. Biochemistry. 1995 Feb 7;34(5):1750–1759. doi: 10.1021/bi00005a032. [DOI] [PubMed] [Google Scholar]
  35. Manley J. L., Takagaki Y. The end of the message--another link between yeast and mammals. Science. 1996 Nov 29;274(5292):1481–1482. doi: 10.1126/science.274.5292.1481. [DOI] [PubMed] [Google Scholar]
  36. McCracken S., Fong N., Yankulov K., Ballantyne S., Pan G., Greenblatt J., Patterson S. D., Wickens M., Bentley D. L. The C-terminal domain of RNA polymerase II couples mRNA processing to transcription. Nature. 1997 Jan 23;385(6614):357–361. doi: 10.1038/385357a0. [DOI] [PubMed] [Google Scholar]
  37. Minvielle-Sebastia L., Preker P. J., Keller W. RNA14 and RNA15 proteins as components of a yeast pre-mRNA 3'-end processing factor. Science. 1994 Dec 9;266(5191):1702–1705. doi: 10.1126/science.7992054. [DOI] [PubMed] [Google Scholar]
  38. 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]
  39. Proudfoot N. J. How RNA polymerase II terminates transcription in higher eukaryotes. Trends Biochem Sci. 1989 Mar;14(3):105–110. doi: 10.1016/0968-0004(89)90132-1. [DOI] [PubMed] [Google Scholar]
  40. Russo P., Li W. Z., Guo Z., Sherman F. Signals that produce 3' termini in CYC1 mRNA of the yeast Saccharomyces cerevisiae. Mol Cell Biol. 1993 Dec;13(12):7836–7849. doi: 10.1128/mcb.13.12.7836. [DOI] [PMC free article] [PubMed] [Google Scholar]
  41. Russo P. Saccharomyces cerevisiae mRNA 3' end forming signals are also involved in transcription termination. Yeast. 1995 Apr 30;11(5):447–453. doi: 10.1002/yea.320110507. [DOI] [PubMed] [Google Scholar]
  42. Russo P., Sherman F. Transcription terminates near the poly(A) site in the CYC1 gene of the yeast Saccharomyces cerevisiae. Proc Natl Acad Sci U S A. 1989 Nov;86(21):8348–8352. doi: 10.1073/pnas.86.21.8348. [DOI] [PMC free article] [PubMed] [Google Scholar]
  43. Sachs A. B., Sarnow P., Hentze M. W. Starting at the beginning, middle, and end: translation initiation in eukaryotes. Cell. 1997 Jun 13;89(6):831–838. doi: 10.1016/s0092-8674(00)80268-8. [DOI] [PubMed] [Google Scholar]
  44. Sadhale P. P., Platt T. Unusual aspects of in vitro RNA processing in the 3' regions of the GAL1, GAL7, and GAL10 genes in Saccharomyces cerevisiae. Mol Cell Biol. 1992 Oct;12(10):4262–4270. doi: 10.1128/mcb.12.10.4262. [DOI] [PMC free article] [PubMed] [Google Scholar]
  45. Sanger F., Nicklen S., Coulson A. R. DNA sequencing with chain-terminating inhibitors. Proc Natl Acad Sci U S A. 1977 Dec;74(12):5463–5467. doi: 10.1073/pnas.74.12.5463. [DOI] [PMC free article] [PubMed] [Google Scholar]
  46. Sikorski R. S., Hieter P. A system of shuttle vectors and yeast host strains designed for efficient manipulation of DNA in Saccharomyces cerevisiae. Genetics. 1989 May;122(1):19–27. doi: 10.1093/genetics/122.1.19. [DOI] [PMC free article] [PubMed] [Google Scholar]
  47. 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]
  48. Takagaki Y., Manley J. L. RNA recognition by the human polyadenylation factor CstF. Mol Cell Biol. 1997 Jul;17(7):3907–3914. doi: 10.1128/mcb.17.7.3907. [DOI] [PMC free article] [PubMed] [Google Scholar]
  49. Wahle E., Keller W. The biochemistry of polyadenylation. Trends Biochem Sci. 1996 Jul;21(7):247–250. [PubMed] [Google Scholar]
  50. Warner J. R. Labeling of RNA and phosphoproteins in Saccharomyces cerevisiae. Methods Enzymol. 1991;194:423–428. doi: 10.1016/0076-6879(91)94033-9. [DOI] [PubMed] [Google Scholar]
  51. Yarger J. G., Armilei G., Gorman M. C. Transcription terminator-like element within a Saccharomyces cerevisiae promoter region. Mol Cell Biol. 1986 Apr;6(4):1095–1101. doi: 10.1128/mcb.6.4.1095. [DOI] [PMC free article] [PubMed] [Google Scholar]
  52. Zitomer R. S., Hall B. D. Yeast cytochrome c messenger RNA. In vitro translation and specific immunoprecipitation of the CYC1 gene product. J Biol Chem. 1976 Oct 25;251(20):6320–6326. [PubMed] [Google Scholar]
  53. Zuker M., Stiegler P. Optimal computer folding of large RNA sequences using thermodynamics and auxiliary information. Nucleic Acids Res. 1981 Jan 10;9(1):133–148. doi: 10.1093/nar/9.1.133. [DOI] [PMC free article] [PubMed] [Google Scholar]
  54. del Olmo M., Pérez-Ortín J. E. A natural A/T-rich sequence from the yeast FBP1 gene exists as a cruciform in Escherichia coli cells. Plasmid. 1993 May;29(3):222–232. doi: 10.1006/plas.1993.1024. [DOI] [PubMed] [Google Scholar]

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