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. 1997 Oct 15;16(20):6263–6271. doi: 10.1093/emboj/16.20.6263

Interplay of yeast global transcriptional regulators Ssn6p-Tup1p and Swi-Snf and their effect on chromatin structure.

I M Gavin 1, R T Simpson 1
PMCID: PMC1326310  PMID: 9321405

Abstract

Transcriptional regulation in yeast involves a number of general trans-acting factors affecting chromatin structure. The Swi-Snf complex is required for expression of a large number of genes and has the ability to remodel chromatin in vitro. The Ssn6p-Tup1p repressor complex may be involved in chromatin organization through the interaction with pathway-specific DNA-binding proteins. To study the interplay of these factors and their effect on chromatin we have analyzed SUC2 chromatin structure in wild-type cells and in strains bearing combinations of ssn6/tup1 and swi1 mutations. We have mapped nucleosome positioning of the repressed gene in wild-type cells using primer extension methodology, allowing base pair resolution, and have analyzed details of chromatin remodeling in the derepressed state. In ssn6 or tup1 mutants under repressing conditions the observed changes in SUC2 chromatin structure may be suppressed by the swi1 mutation, suggesting that Ssn6p-Tup1p is not required for the establishment of nucleosome positioning at the SUC2 promoter. Our data indicate the involvement of chromatin remodeling factors distinct from the Swi-Snf complex in SUC2 transcriptional regulation and suggest that Swi-Snf may antagonize Ssn6p-Tup1p by controlling remodeling activity. We also show that a relatively high level of SUC2 transcription can coexist with positioned nucleosomes.

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Selected References

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  1. Balasubramanian B., Lowry C. V., Zitomer R. S. The Rox1 repressor of the Saccharomyces cerevisiae hypoxic genes is a specific DNA-binding protein with a high-mobility-group motif. Mol Cell Biol. 1993 Oct;13(10):6071–6078. doi: 10.1128/mcb.13.10.6071. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Bortvin A., Winston F. Evidence that Spt6p controls chromatin structure by a direct interaction with histones. Science. 1996 Jun 7;272(5267):1473–1476. doi: 10.1126/science.272.5267.1473. [DOI] [PubMed] [Google Scholar]
  3. Carlson M., Botstein D. Two differentially regulated mRNAs with different 5' ends encode secreted with intracellular forms of yeast invertase. Cell. 1982 Jan;28(1):145–154. doi: 10.1016/0092-8674(82)90384-1. [DOI] [PubMed] [Google Scholar]
  4. Carlson M., Taussig R., Kustu S., Botstein D. The secreted form of invertase in Saccharomyces cerevisiae is synthesized from mRNA encoding a signal sequence. Mol Cell Biol. 1983 Mar;3(3):439–447. doi: 10.1128/mcb.3.3.439. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. Cereghino G. P., Scheffler I. E. Genetic analysis of glucose regulation in saccharomyces cerevisiae: control of transcription versus mRNA turnover. EMBO J. 1996 Jan 15;15(2):363–374. [PMC free article] [PubMed] [Google Scholar]
  6. Church G. M., Gilbert W. Genomic sequencing. Proc Natl Acad Sci U S A. 1984 Apr;81(7):1991–1995. doi: 10.1073/pnas.81.7.1991. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. Cooper J. P., Roth S. Y., Simpson R. T. The global transcriptional regulators, SSN6 and TUP1, play distinct roles in the establishment of a repressive chromatin structure. Genes Dev. 1994 Jun 15;8(12):1400–1410. doi: 10.1101/gad.8.12.1400. [DOI] [PubMed] [Google Scholar]
  8. Côté J., Quinn J., Workman J. L., Peterson C. L. Stimulation of GAL4 derivative binding to nucleosomal DNA by the yeast SWI/SNF complex. Science. 1994 Jul 1;265(5168):53–60. doi: 10.1126/science.8016655. [DOI] [PubMed] [Google Scholar]
  9. Edmondson D. G., Roth S. Y. Chromatin and transcription. FASEB J. 1996 Aug;10(10):1173–1182. doi: 10.1096/fasebj.10.10.8751719. [DOI] [PubMed] [Google Scholar]
  10. Edmondson D. G., Smith M. M., Roth S. Y. Repression domain of the yeast global repressor Tup1 interacts directly with histones H3 and H4. Genes Dev. 1996 May 15;10(10):1247–1259. doi: 10.1101/gad.10.10.1247. [DOI] [PubMed] [Google Scholar]
  11. Elledge S. J., Zhou Z., Allen J. B., Navas T. A. DNA damage and cell cycle regulation of ribonucleotide reductase. Bioessays. 1993 May;15(5):333–339. doi: 10.1002/bies.950150507. [DOI] [PubMed] [Google Scholar]
  12. Friesen H., Hepworth S. R., Segall J. An Ssn6-Tup1-dependent negative regulatory element controls sporulation-specific expression of DIT1 and DIT2 in Saccharomyces cerevisiae. Mol Cell Biol. 1997 Jan;17(1):123–134. doi: 10.1128/mcb.17.1.123. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. Grunstein M., Hecht A., Fisher-Adams G., Wan J., Mann R. K., Strahl-Bolsinger S., Laroche T., Gasser S. The regulation of euchromatin and heterochromatin by histones in yeast. J Cell Sci Suppl. 1995;19:29–36. doi: 10.1242/jcs.1995.supplement_19.4. [DOI] [PubMed] [Google Scholar]
  14. Herschbach B. M., Arnaud M. B., Johnson A. D. Transcriptional repression directed by the yeast alpha 2 protein in vitro. Nature. 1994 Jul 28;370(6487):309–311. doi: 10.1038/370309a0. [DOI] [PubMed] [Google Scholar]
  15. Hill J., Donald K. A., Griffiths D. E., Donald G. DMSO-enhanced whole cell yeast transformation. Nucleic Acids Res. 1991 Oct 25;19(20):5791–5791. doi: 10.1093/nar/19.20.5791. [DOI] [PMC free article] [PubMed] [Google Scholar]
  16. Hirschhorn J. N., Bortvin A. L., Ricupero-Hovasse S. L., Winston F. A new class of histone H2A mutations in Saccharomyces cerevisiae causes specific transcriptional defects in vivo. Mol Cell Biol. 1995 Apr;15(4):1999–2009. doi: 10.1128/mcb.15.4.1999. [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. 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]
  18. Keleher C. A., Redd M. J., Schultz J., Carlson M., Johnson A. D. Ssn6-Tup1 is a general repressor of transcription in yeast. Cell. 1992 Feb 21;68(4):709–719. doi: 10.1016/0092-8674(92)90146-4. [DOI] [PubMed] [Google Scholar]
  19. Kingston R. E., Bunker C. A., Imbalzano A. N. Repression and activation by multiprotein complexes that alter chromatin structure. Genes Dev. 1996 Apr 15;10(8):905–920. doi: 10.1101/gad.10.8.905. [DOI] [PubMed] [Google Scholar]
  20. Komachi K., Redd M. J., Johnson A. D. The WD repeats of Tup1 interact with the homeo domain protein alpha 2. Genes Dev. 1994 Dec 1;8(23):2857–2867. doi: 10.1101/gad.8.23.2857. [DOI] [PubMed] [Google Scholar]
  21. Kruger W., Peterson C. L., Sil A., Coburn C., Arents G., Moudrianakis E. N., Herskowitz I. Amino acid substitutions in the structured domains of histones H3 and H4 partially relieve the requirement of the yeast SWI/SNF complex for transcription. Genes Dev. 1995 Nov 15;9(22):2770–2779. doi: 10.1101/gad.9.22.2770. [DOI] [PubMed] [Google Scholar]
  22. Lu Q., Wallrath L. L., Elgin S. C. Nucleosome positioning and gene regulation. J Cell Biochem. 1994 May;55(1):83–92. doi: 10.1002/jcb.240550110. [DOI] [PubMed] [Google Scholar]
  23. Lutfiyya L. L., Johnston M. Two zinc-finger-containing repressors are responsible for glucose repression of SUC2 expression. Mol Cell Biol. 1996 Sep;16(9):4790–4797. doi: 10.1128/mcb.16.9.4790. [DOI] [PMC free article] [PubMed] [Google Scholar]
  24. Matallana E., Franco L., Pérez-Ortín J. E. Chromatin structure of the yeast SUC2 promoter in regulatory mutants. Mol Gen Genet. 1992 Feb;231(3):395–400. doi: 10.1007/BF00292708. [DOI] [PubMed] [Google Scholar]
  25. Mukai Y., Harashima S., Oshima Y. AAR1/TUP1 protein, with a structure similar to that of the beta subunit of G proteins, is required for a1-alpha 2 and alpha 2 repression in cell type control of Saccharomyces cerevisiae. Mol Cell Biol. 1991 Jul;11(7):3773–3779. doi: 10.1128/mcb.11.7.3773. [DOI] [PMC free article] [PubMed] [Google Scholar]
  26. Nehlin J. O., Carlberg M., Ronne H. Yeast SKO1 gene encodes a bZIP protein that binds to the CRE motif and acts as a repressor of transcription. Nucleic Acids Res. 1992 Oct 25;20(20):5271–5278. doi: 10.1093/nar/20.20.5271. [DOI] [PMC free article] [PubMed] [Google Scholar]
  27. Nehlin J. O., Ronne H. Yeast MIG1 repressor is related to the mammalian early growth response and Wilms' tumour finger proteins. EMBO J. 1990 Sep;9(9):2891–2898. doi: 10.1002/j.1460-2075.1990.tb07479.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  28. Owen-Hughes T., Utley R. T., Côté J., Peterson C. L., Workman J. L. Persistent site-specific remodeling of a nucleosome array by transient action of the SWI/SNF complex. Science. 1996 Jul 26;273(5274):513–516. doi: 10.1126/science.273.5274.513. [DOI] [PubMed] [Google Scholar]
  29. 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]
  30. Peterson C. L. Multiple SWItches to turn on chromatin? Curr Opin Genet Dev. 1996 Apr;6(2):171–175. doi: 10.1016/s0959-437x(96)80047-5. [DOI] [PubMed] [Google Scholar]
  31. Peterson C. L., Tamkun J. W. The SWI-SNF complex: a chromatin remodeling machine? Trends Biochem Sci. 1995 Apr;20(4):143–146. doi: 10.1016/s0968-0004(00)88990-2. [DOI] [PubMed] [Google Scholar]
  32. Pérez-Ortín J. E., Estruch F., Matallana E., Franco L. Fine analysis of the chromatin structure of the yeast SUC2 gene and of its changes upon derepression. Comparison between the chromosomal and plasmid-inserted genes. Nucleic Acids Res. 1987 Sep 11;15(17):6937–6956. doi: 10.1093/nar/15.17.6937. [DOI] [PMC free article] [PubMed] [Google Scholar]
  33. Redd M. J., Arnaud M. B., Johnson A. D. A complex composed of tup1 and ssn6 represses transcription in vitro. J Biol Chem. 1997 Apr 25;272(17):11193–11197. doi: 10.1074/jbc.272.17.11193. [DOI] [PubMed] [Google Scholar]
  34. Redd M. J., Stark M. R., Johnson A. D. Accessibility of alpha 2-repressed promoters to the activator Gal4. Mol Cell Biol. 1996 Jun;16(6):2865–2869. doi: 10.1128/mcb.16.6.2865. [DOI] [PMC free article] [PubMed] [Google Scholar]
  35. Reyes J. C., Muchardt C., Yaniv M. Components of the human SWI/SNF complex are enriched in active chromatin and are associated with the nuclear matrix. J Cell Biol. 1997 Apr 21;137(2):263–274. doi: 10.1083/jcb.137.2.263. [DOI] [PMC free article] [PubMed] [Google Scholar]
  36. Roth S. Y. Chromatin-mediated transcriptional repression in yeast. Curr Opin Genet Dev. 1995 Apr;5(2):168–173. doi: 10.1016/0959-437x(95)80004-2. [DOI] [PubMed] [Google Scholar]
  37. Roth S. Y., Shimizu M., Johnson L., Grunstein M., Simpson R. T. Stable nucleosome positioning and complete repression by the yeast alpha 2 repressor are disrupted by amino-terminal mutations in histone H4. Genes Dev. 1992 Mar;6(3):411–425. doi: 10.1101/gad.6.3.411. [DOI] [PubMed] [Google Scholar]
  38. Roth S. Y., Simpson R. T. Yeast minichromosomes. Methods Cell Biol. 1991;35:289–314. [PubMed] [Google Scholar]
  39. Rothstein R. Targeting, disruption, replacement, and allele rescue: integrative DNA transformation in yeast. Methods Enzymol. 1991;194:281–301. doi: 10.1016/0076-6879(91)94022-5. [DOI] [PubMed] [Google Scholar]
  40. Sarokin L., Carlson M. Upstream region required for regulated expression of the glucose-repressible SUC2 gene of Saccharomyces cerevisiae. Mol Cell Biol. 1984 Dec;4(12):2750–2757. doi: 10.1128/mcb.4.12.2750. [DOI] [PMC free article] [PubMed] [Google Scholar]
  41. Sherman F. Getting started with yeast. Methods Enzymol. 1991;194:3–21. doi: 10.1016/0076-6879(91)94004-v. [DOI] [PubMed] [Google Scholar]
  42. Shimizu M., Roth S. Y., Szent-Gyorgyi C., Simpson R. T. Nucleosomes are positioned with base pair precision adjacent to the alpha 2 operator in Saccharomyces cerevisiae. EMBO J. 1991 Oct;10(10):3033–3041. doi: 10.1002/j.1460-2075.1991.tb07854.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  43. 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]
  44. Simpson R. T., Roth S. Y., Morse R. H., Patterton H. G., Cooper J. P., Murphy M., Kladde M. P., Shimizu M. Nucleosome positioning and transcription. Cold Spring Harb Symp Quant Biol. 1993;58:237–245. doi: 10.1101/sqb.1993.058.01.028. [DOI] [PubMed] [Google Scholar]
  45. Svaren J., Hörz W. Transcription factors vs nucleosomes: regulation of the PHO5 promoter in yeast. Trends Biochem Sci. 1997 Mar;22(3):93–97. doi: 10.1016/s0968-0004(97)01001-3. [DOI] [PubMed] [Google Scholar]
  46. Szeto L., Broach J. R. Role of alpha2 protein in donor locus selection during mating type interconversion. Mol Cell Biol. 1997 Feb;17(2):751–759. doi: 10.1128/mcb.17.2.751. [DOI] [PMC free article] [PubMed] [Google Scholar]
  47. Teunissen A. W., van den Berg J. A., Steensma H. Y. Transcriptional regulation of flocculation genes in Saccharomyces cerevisiae. Yeast. 1995 Apr 30;11(5):435–446. doi: 10.1002/yea.320110506. [DOI] [PubMed] [Google Scholar]
  48. Tillman T. S., Ganster R. W., Jiang R., Carlson M., Schmidt M. C. STD1 (MSN3) interacts directly with the TATA-binding protein and modulates transcription of the SUC2 gene of Saccharomyces cerevisiae. Nucleic Acids Res. 1995 Aug 25;23(16):3174–3180. doi: 10.1093/nar/23.16.3174. [DOI] [PMC free article] [PubMed] [Google Scholar]
  49. Treitel M. A., Carlson M. Repression by SSN6-TUP1 is directed by MIG1, a repressor/activator protein. Proc Natl Acad Sci U S A. 1995 Apr 11;92(8):3132–3136. doi: 10.1073/pnas.92.8.3132. [DOI] [PMC free article] [PubMed] [Google Scholar]
  50. Trumbly R. J. Glucose repression in the yeast Saccharomyces cerevisiae. Mol Microbiol. 1992 Jan;6(1):15–21. doi: 10.1111/j.1365-2958.1992.tb00832.x. [DOI] [PubMed] [Google Scholar]
  51. Tzamarias D., Struhl K. Distinct TPR motifs of Cyc8 are involved in recruiting the Cyc8-Tup1 corepressor complex to differentially regulated promoters. Genes Dev. 1995 Apr 1;9(7):821–831. doi: 10.1101/gad.9.7.821. [DOI] [PubMed] [Google Scholar]
  52. Tzamarias D., Struhl K. Functional dissection of the yeast Cyc8-Tup1 transcriptional co-repressor complex. Nature. 1994 Jun 30;369(6483):758–761. doi: 10.1038/369758a0. [DOI] [PubMed] [Google Scholar]
  53. Vallier L. G., Carlson M. Synergistic release from glucose repression by mig1 and ssn mutations in Saccharomyces cerevisiae. Genetics. 1994 May;137(1):49–54. doi: 10.1093/genetics/137.1.49. [DOI] [PMC free article] [PubMed] [Google Scholar]
  54. Varanasi U. S., Klis M., Mikesell P. B., Trumbly R. J. The Cyc8 (Ssn6)-Tup1 corepressor complex is composed of one Cyc8 and four Tup1 subunits. Mol Cell Biol. 1996 Dec;16(12):6707–6714. doi: 10.1128/mcb.16.12.6707. [DOI] [PMC free article] [PubMed] [Google Scholar]
  55. Verdone L., Camilloni G., Di Mauro E., Caserta M. Chromatin remodeling during Saccharomyces cerevisiae ADH2 gene activation. Mol Cell Biol. 1996 May;16(5):1978–1988. doi: 10.1128/mcb.16.5.1978. [DOI] [PMC free article] [PubMed] [Google Scholar]
  56. Weiss K., Simpson R. T. Cell type-specific chromatin organization of the region that governs directionality of yeast mating type switching. EMBO J. 1997 Jul 16;16(14):4352–4360. doi: 10.1093/emboj/16.14.4352. [DOI] [PMC free article] [PubMed] [Google Scholar]
  57. Williams F. E., Trumbly R. J. Characterization of TUP1, a mediator of glucose repression in Saccharomyces cerevisiae. Mol Cell Biol. 1990 Dec;10(12):6500–6511. doi: 10.1128/mcb.10.12.6500. [DOI] [PMC free article] [PubMed] [Google Scholar]
  58. Williams F. E., Varanasi U., Trumbly R. J. The CYC8 and TUP1 proteins involved in glucose repression in Saccharomyces cerevisiae are associated in a protein complex. Mol Cell Biol. 1991 Jun;11(6):3307–3316. doi: 10.1128/mcb.11.6.3307. [DOI] [PMC free article] [PubMed] [Google Scholar]
  59. Wilson C. J., Chao D. M., Imbalzano A. N., Schnitzler G. R., Kingston R. E., Young R. A. RNA polymerase II holoenzyme contains SWI/SNF regulators involved in chromatin remodeling. Cell. 1996 Jan 26;84(2):235–244. doi: 10.1016/s0092-8674(00)80978-2. [DOI] [PubMed] [Google Scholar]
  60. Winston F., Carlson M. Yeast SNF/SWI transcriptional activators and the SPT/SIN chromatin connection. Trends Genet. 1992 Nov;8(11):387–391. doi: 10.1016/0168-9525(92)90300-s. [DOI] [PubMed] [Google Scholar]
  61. Zitomer R. S., Lowry C. V. Regulation of gene expression by oxygen in Saccharomyces cerevisiae. Microbiol Rev. 1992 Mar;56(1):1–11. doi: 10.1128/mr.56.1.1-11.1992. [DOI] [PMC free article] [PubMed] [Google Scholar]

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