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. 1994 Aug;14(8):5229–5241. doi: 10.1128/mcb.14.8.5229

Chromatin structure modulation in Saccharomyces cerevisiae by centromere and promoter factor 1.

N A Kent 1, J S Tsang 1, D J Crowther 1, J Mellor 1
PMCID: PMC359042  PMID: 8035802

Abstract

CPF1 is an abundant basic-helix-loop-helix-ZIP protein that binds to the CDEI motif in Saccharomyces cerevisiae centromeres and in the promoters of numerous genes, including those encoding enzymes of the methionine biosynthetic pathway. Strains lacking CPF1 are methionine auxotrophs, and it has been proposed that CPF1 might positively influence transcription at the MET25 and MET16 genes by modulating promoter chromatin structure. We test this hypothesis and show that the regions surrounding the CDEI motifs in the MET25 and MET16 promoters are maintained in a nucleosome-free state and that this requires the entire CPF1 protein. However, the chromatin structure around the CDEI motifs does not change on derepression of transcription and does not correlate with the methionine phenotype of the cell. An intact CDEI motif but not CPF1 is required for transcriptional activation from a region of the MET25 upstream activation sequence. Our results suggest that CPF1 functions to modulate chromatin structure around the CDEI motif but that these changes at the MET25 and MET16 promoters do not explain how CPF1 functions to maintain methionine-independent growth. The presence of CPF1-dependent chromatin structures at these promoters leads to a weak repression of transcription.

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Selected References

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

  1. Axelrod J. D., Reagan M. S., Majors J. GAL4 disrupts a repressing nucleosome during activation of GAL1 transcription in vivo. Genes Dev. 1993 May;7(5):857–869. doi: 10.1101/gad.7.5.857. [DOI] [PubMed] [Google Scholar]
  2. Baker R. E., Masison D. C. Isolation of the gene encoding the Saccharomyces cerevisiae centromere-binding protein CP1. Mol Cell Biol. 1990 Jun;10(6):2458–2467. doi: 10.1128/mcb.10.6.2458. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Beckmann H., Kadesch T. The leucine zipper of TFE3 dictates helix-loop-helix dimerization specificity. Genes Dev. 1991 Jun;5(6):1057–1066. doi: 10.1101/gad.5.6.1057. [DOI] [PubMed] [Google Scholar]
  4. Blackwood E. M., Eisenman R. N. Max: a helix-loop-helix zipper protein that forms a sequence-specific DNA-binding complex with Myc. Science. 1991 Mar 8;251(4998):1211–1217. doi: 10.1126/science.2006410. [DOI] [PubMed] [Google Scholar]
  5. Bram R. J., Kornberg R. D. Isolation of a Saccharomyces cerevisiae centromere DNA-binding protein, its human homolog, and its possible role as a transcription factor. Mol Cell Biol. 1987 Jan;7(1):403–409. doi: 10.1128/mcb.7.1.403. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. Cai M., Davis R. W. Yeast centromere binding protein CBF1, of the helix-loop-helix protein family, is required for chromosome stability and methionine prototrophy. Cell. 1990 May 4;61(3):437–446. doi: 10.1016/0092-8674(90)90525-j. [DOI] [PubMed] [Google Scholar]
  7. Chasman D. I., Lue N. F., Buchman A. R., LaPointe J. W., Lorch Y., Kornberg R. D. A yeast protein that influences the chromatin structure of UASG and functions as a powerful auxiliary gene activator. Genes Dev. 1990 Apr;4(4):503–514. doi: 10.1101/gad.4.4.503. [DOI] [PubMed] [Google Scholar]
  8. Cherest H., Thomas D., Surdin-Kerjan Y. Nucleotide sequence of the MET8 gene of Saccharomyces cerevisiae. Nucleic Acids Res. 1990 Feb 11;18(3):659–659. doi: 10.1093/nar/18.3.659. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. Croston G. E., Laybourn P. J., Paranjape S. M., Kadonaga J. T. Mechanism of transcriptional antirepression by GAL4-VP16. Genes Dev. 1992 Dec;6(12A):2270–2281. doi: 10.1101/gad.6.12a.2270. [DOI] [PubMed] [Google Scholar]
  10. Cumberledge S., Carbon J. Mutational analysis of meiotic and mitotic centromere function in Saccharomyces cerevisiae. Genetics. 1987 Oct;117(2):203–212. doi: 10.1093/genetics/117.2.203. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. Dang C. V., Dolde C., Gillison M. L., Kato G. J. Discrimination between related DNA sites by a single amino acid residue of Myc-related basic-helix-loop-helix proteins. Proc Natl Acad Sci U S A. 1992 Jan 15;89(2):599–602. doi: 10.1073/pnas.89.2.599. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. Dang C. V., McGuire M., Buckmire M., Lee W. M. Involvement of the 'leucine zipper' region in the oligomerization and transforming activity of human c-myc protein. Nature. 1989 Feb 16;337(6208):664–666. doi: 10.1038/337664a0. [DOI] [PubMed] [Google Scholar]
  13. Dowell S. J., Tsang J. S., Mellor J. The centromere and promoter factor 1 of yeast contains a dimerisation domain located carboxy-terminal to the bHLH domain. Nucleic Acids Res. 1992 Aug 25;20(16):4229–4236. doi: 10.1093/nar/20.16.4229. [DOI] [PMC free article] [PubMed] [Google Scholar]
  14. Fascher K. D., Schmitz J., Hörz W. Structural and functional requirements for the chromatin transition at the PHO5 promoter in Saccharomyces cerevisiae upon PHO5 activation. J Mol Biol. 1993 Jun 5;231(3):658–667. doi: 10.1006/jmbi.1993.1317. [DOI] [PubMed] [Google Scholar]
  15. Fedor M. J., Lue N. F., Kornberg R. D. Statistical positioning of nucleosomes by specific protein-binding to an upstream activating sequence in yeast. J Mol Biol. 1988 Nov 5;204(1):109–127. doi: 10.1016/0022-2836(88)90603-1. [DOI] [PubMed] [Google Scholar]
  16. Ferré-D'Amaré A. R., Pognonec P., Roeder R. G., Burley S. K. Structure and function of the b/HLH/Z domain of USF. EMBO J. 1994 Jan 1;13(1):180–189. doi: 10.1002/j.1460-2075.1994.tb06247.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. Fisher F., Goding C. R. Single amino acid substitutions alter helix-loop-helix protein specificity for bases flanking the core CANNTG motif. EMBO J. 1992 Nov;11(11):4103–4109. doi: 10.1002/j.1460-2075.1992.tb05503.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  18. Foreman P. K., Davis R. W. Point mutations that separate the role of Saccharomyces cerevisiae centromere binding factor 1 in chromosome segregation from its role in transcriptional activation. Genetics. 1993 Oct;135(2):287–296. doi: 10.1093/genetics/135.2.287. [DOI] [PMC free article] [PubMed] [Google Scholar]
  19. Gilbert D. M., Losson R., Chambon P. Ligand dependence of estrogen receptor induced changes in chromatin structure. Nucleic Acids Res. 1992 Sep 11;20(17):4525–4531. doi: 10.1093/nar/20.17.4525. [DOI] [PMC free article] [PubMed] [Google Scholar]
  20. Gregor P. D., Sawadogo M., Roeder R. G. The adenovirus major late transcription factor USF is a member of the helix-loop-helix group of regulatory proteins and binds to DNA as a dimer. Genes Dev. 1990 Oct;4(10):1730–1740. doi: 10.1101/gad.4.10.1730. [DOI] [PubMed] [Google Scholar]
  21. 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]
  22. Hirschhorn J. N., Brown S. A., Clark C. D., Winston F. Evidence that SNF2/SWI2 and SNF5 activate transcription in yeast by altering chromatin structure. Genes Dev. 1992 Dec;6(12A):2288–2298. doi: 10.1101/gad.6.12a.2288. [DOI] [PubMed] [Google Scholar]
  23. Hu Y. F., Lüscher B., Admon A., Mermod N., Tjian R. Transcription factor AP-4 contains multiple dimerization domains that regulate dimer specificity. Genes Dev. 1990 Oct;4(10):1741–1752. doi: 10.1101/gad.4.10.1741. [DOI] [PubMed] [Google Scholar]
  24. Kent N. A., Bird L. E., Mellor J. Chromatin analysis in yeast using NP-40 permeabilised sphaeroplasts. Nucleic Acids Res. 1993 Sep 25;21(19):4653–4654. doi: 10.1093/nar/21.19.4653. [DOI] [PMC free article] [PubMed] [Google Scholar]
  25. Kerjan P., Cherest H., Surdin-Kerjan Y. Nucleotide sequence of the Saccharomyces cerevisiae MET25 gene. Nucleic Acids Res. 1986 Oct 24;14(20):7861–7871. doi: 10.1093/nar/14.20.7861. [DOI] [PMC free article] [PubMed] [Google Scholar]
  26. Korch C., Mountain H. A., Byström A. S. Cloning, nucleotide sequence, and regulation of MET14, the gene encoding the APS kinase of Saccharomyces cerevisiae. Mol Gen Genet. 1991 Sep;229(1):96–108. doi: 10.1007/BF00264218. [DOI] [PubMed] [Google Scholar]
  27. Masison D. C., Baker R. E. Meiosis in Saccharomyces cerevisiae mutants lacking the centromere-binding protein CP1. Genetics. 1992 May;131(1):43–53. doi: 10.1093/genetics/131.1.43. [DOI] [PMC free article] [PubMed] [Google Scholar]
  28. Masison D. C., O'Connell K. F., Baker R. E. Mutational analysis of the Saccharomyces cerevisiae general regulatory factor CP1. Nucleic Acids Res. 1993 Aug 25;21(17):4133–4141. doi: 10.1093/nar/21.17.4133. [DOI] [PMC free article] [PubMed] [Google Scholar]
  29. McKenzie E. A., Kent N. A., Dowell S. J., Moreno F., Bird L. E., Mellor J. The centromere and promoter factor, 1, CPF1, of Saccharomyces cerevisiae modulates gene activity through a family of factors including SPT21, RPD1 (SIN3), RPD3 and CCR4. Mol Gen Genet. 1993 Sep;240(3):374–386. doi: 10.1007/BF00280389. [DOI] [PubMed] [Google Scholar]
  30. Mellor J., Jiang W., Funk M., Rathjen J., Barnes C. A., Hinz T., Hegemann J. H., Philippsen P. CPF1, a yeast protein which functions in centromeres and promoters. EMBO J. 1990 Dec;9(12):4017–4026. doi: 10.1002/j.1460-2075.1990.tb07623.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  31. Mellor J., Rathjen J., Jiang W., Barnes C. A., Dowell S. J. DNA binding of CPF1 is required for optimal centromere function but not for maintaining methionine prototrophy in yeast. Nucleic Acids Res. 1991 Jun 11;19(11):2961–2969. doi: 10.1093/nar/19.11.2961. [DOI] [PMC free article] [PubMed] [Google Scholar]
  32. Natsoulis G., Dollard C., Winston F., Boeke J. D. The products of the SPT10 and SPT21 genes of Saccharomyces cerevisiae increase the amplitude of transcriptional regulation at a large number of unlinked loci. New Biol. 1991 Dec;3(12):1249–1259. [PubMed] [Google Scholar]
  33. Niedenthal R. K., Sen-Gupta M., Wilmen A., Hegemann J. H. Cpf1 protein induced bending of yeast centromere DNA element I. Nucleic Acids Res. 1993 Oct 11;21(20):4726–4733. doi: 10.1093/nar/21.20.4726. [DOI] [PMC free article] [PubMed] [Google Scholar]
  34. O'Connell K. F., Baker R. E. Possible cross-regulation of phosphate and sulfate metabolism in Saccharomyces cerevisiae. Genetics. 1992 Sep;132(1):63–73. doi: 10.1093/genetics/132.1.63. [DOI] [PMC free article] [PubMed] [Google Scholar]
  35. Peterson C. L., Herskowitz I. Characterization of the yeast SWI1, SWI2, and SWI3 genes, which encode a global activator of transcription. Cell. 1992 Feb 7;68(3):573–583. doi: 10.1016/0092-8674(92)90192-f. [DOI] [PubMed] [Google Scholar]
  36. Pham T. A., Hwung Y. P., McDonnell D. P., O'Malley B. W. Transactivation functions facilitate the disruption of chromatin structure by estrogen receptor derivatives in vivo. J Biol Chem. 1991 Sep 25;266(27):18179–18187. [PubMed] [Google Scholar]
  37. Pérez-Ortín J. E., Estruch F., Matallana E., Franco L. Sliding-end-labelling. A method to avoid artifacts in nucleosome positioning. FEBS Lett. 1986 Nov 10;208(1):31–33. doi: 10.1016/0014-5793(86)81525-3. [DOI] [PubMed] [Google Scholar]
  38. Stewart A. F., Reik A., Schütz G. A simpler and better method to cleave chromatin with DNase 1 for hypersensitive site analyses. Nucleic Acids Res. 1991 Jun 11;19(11):3157–3157. doi: 10.1093/nar/19.11.3157. [DOI] [PMC free article] [PubMed] [Google Scholar]
  39. Struhl K. Nucleotide sequence and transcriptional mapping of the yeast pet56-his3-ded1 gene region. Nucleic Acids Res. 1985 Dec 9;13(23):8587–8601. doi: 10.1093/nar/13.23.8587. [DOI] [PMC free article] [PubMed] [Google Scholar]
  40. Svaren J., Hörz W. Histones, nucleosomes and transcription. Curr Opin Genet Dev. 1993 Apr;3(2):219–225. doi: 10.1016/0959-437x(93)90026-l. [DOI] [PubMed] [Google Scholar]
  41. Thomas D., Barbey R., Surdin-Kerjan Y. Gene-enzyme relationship in the sulfate assimilation pathway of Saccharomyces cerevisiae. Study of the 3'-phosphoadenylylsulfate reductase structural gene. J Biol Chem. 1990 Sep 15;265(26):15518–15524. [PubMed] [Google Scholar]
  42. Thomas D., Cherest H., Surdin-Kerjan Y. Elements involved in S-adenosylmethionine-mediated regulation of the Saccharomyces cerevisiae MET25 gene. Mol Cell Biol. 1989 Aug;9(8):3292–3298. doi: 10.1128/mcb.9.8.3292. [DOI] [PMC free article] [PubMed] [Google Scholar]
  43. Thomas D., Jacquemin I., Surdin-Kerjan Y. MET4, a leucine zipper protein, and centromere-binding factor 1 are both required for transcriptional activation of sulfur metabolism in Saccharomyces cerevisiae. Mol Cell Biol. 1992 Apr;12(4):1719–1727. doi: 10.1128/mcb.12.4.1719. [DOI] [PMC free article] [PubMed] [Google Scholar]
  44. Tschumper G., Carbon J. Sequence of a yeast DNA fragment containing a chromosomal replicator and the TRP1 gene. Gene. 1980 Jul;10(2):157–166. doi: 10.1016/0378-1119(80)90133-x. [DOI] [PubMed] [Google Scholar]
  45. Vidal M., Strich R., Esposito R. E., Gaber R. F. RPD1 (SIN3/UME4) is required for maximal activation and repression of diverse yeast genes. Mol Cell Biol. 1991 Dec;11(12):6306–6316. doi: 10.1128/mcb.11.12.6306. [DOI] [PMC free article] [PubMed] [Google Scholar]
  46. Wang H., Clark I., Nicholson P. R., Herskowitz I., Stillman D. J. The Saccharomyces cerevisiae SIN3 gene, a negative regulator of HO, contains four paired amphipathic helix motifs. Mol Cell Biol. 1990 Nov;10(11):5927–5936. doi: 10.1128/mcb.10.11.5927. [DOI] [PMC free article] [PubMed] [Google Scholar]
  47. Workman J. L., Kingston R. E. Nucleosome core displacement in vitro via a metastable transcription factor-nucleosome complex. Science. 1992 Dec 11;258(5089):1780–1784. doi: 10.1126/science.1465613. [DOI] [PubMed] [Google Scholar]
  48. Workman J. L., Taylor I. C., Kingston R. E. Activation domains of stably bound GAL4 derivatives alleviate repression of promoters by nucleosomes. Cell. 1991 Feb 8;64(3):533–544. doi: 10.1016/0092-8674(91)90237-s. [DOI] [PubMed] [Google Scholar]
  49. de Winde J. H., Grivell L. A. Global regulation of mitochondrial biogenesis in Saccharomyces cerevisiae: ABF1 and CPF1 play opposite roles in regulating expression of the QCR8 gene, which encodes subunit VIII of the mitochondrial ubiquinol-cytochrome c oxidoreductase. Mol Cell Biol. 1992 Jun;12(6):2872–2883. doi: 10.1128/mcb.12.6.2872. [DOI] [PMC free article] [PubMed] [Google Scholar]

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