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Analysis of Silencing in Saccharomyces cerevisiae

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Part of the book series: Methods in Molecular Biology ((MIMB,volume 1205))

Abstract

Silencing assays have proven to be powerful tools not only for understanding how epigenetic processes function and defining the structural components of silent chromatin, but also for a useful readout for characterizing the functions of proteins involved in chromatin biology that influence epigenetic processes directly or indirectly. This chapter describes a collection of assays for monitoring silencing in Saccharomyces cerevisiae, including qualitative and quantitative methods as well as protocols that provide either indirect or direct measurements of the transcriptional state of loci regulated by silent chromatin.

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References

  1. Rusché LN, Kirchmaier AL, Rine J (2003) The establishment, inheritance, and function of silenced chromatin in Saccharomyces cerevisiae. Annu Rev Biochem 72:481–516

    Article  PubMed  Google Scholar 

  2. Palladino F, Laroche T, Gilson E et al (1993) SIR3 and SIR4 proteins are required for the positioning and integrity of yeast telomeres. Cell 75:543–555

    Article  PubMed  CAS  Google Scholar 

  3. Smith JS, Boeke JD (1997) An unusual form of transcriptional silencing in yeast ribosomal DNA. Genes Dev 11:241–254

    Article  PubMed  CAS  Google Scholar 

  4. Bi X, Broach JR (1997) DNA in transcriptionally silent chromatin assumes a distinct topology that is sensitive to cell cycle progression. Mol Cell Biol 17:7077–7087

    PubMed  CAS  PubMed Central  Google Scholar 

  5. Cheng T-H, Li Y-C, Gartenberg MR (1998) Persistence of an alternate chromatin structure at silenced loci in the absence of silencers. Proc Natl Acad Sci U S A 95:5521–5526

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  6. Weiss K, Simpson RT (1998) High-resolution structural analysis of chromatin at specific loci: Saccharomyces cerevisiae silent mating type locus HMLalpha. Mol Cell Biol 18:5392–5403

    PubMed  CAS  PubMed Central  Google Scholar 

  7. Ravindra A, Weiss K, Simpson RT (1999) High-resolution structural analysis of chromatin at specific loci: Saccharomyces cerevisiae silent mating-type locus HMRa. Mol Cell Biol 19:7944–7950

    PubMed  CAS  PubMed Central  Google Scholar 

  8. Loo S, Rine J (1994) Silencers and domains of generalized repression. Science 264:1768–1771

    Article  PubMed  CAS  Google Scholar 

  9. Gottschling DE (1992) Telomere-proximal DNA in Saccharomyces cerevisiae is refractory to methyltransferase activity in vivo. Proc Natl Acad Sci U S A 89:4062–4065

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  10. Singh J, Klar AJ (1992) Active genes in budding yeast display enhanced in vivo accessibility to foreign DNA methylases: a novel in vivo probe for chromatin structure of yeast. Genes Dev 6:186–196

    Article  PubMed  CAS  Google Scholar 

  11. Rusché LN, Kirchmaier AL, Rine J (2002) Ordered nucleation and spreading of silenced chromatin in Saccharomyces cerevisiae. Mol Biol Cell 13:2207–2222

    Article  PubMed  PubMed Central  Google Scholar 

  12. Hoppe G, Tanny J, Rudner A et al (2002) Steps in assembly of silent chromatin in yeast: Sir3-independent binding of a Sir2/Sir4 complex to silencers and role for Sir2-dependent deacetylation. Mol Cell Biol 22:4167–4180

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  13. Luo K, Vega-Palas MA, Grunstein M (2002) Rap1-Sir4 binding independent of other Sir, yKu or histone interactions initiates the assembly of telomeric heterochromatin in yeast. Genes Dev 16:1528–1539

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  14. Buchberger JR, Onishi M, Li G et al (2008) Sir3-nucleosome interactions in spreading of silent chromatin in Saccharomyces cerevisiae. Mol Cell Biol 28:6903–6918

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  15. Yang B, Kirchmaier AL (2006) Bypassing the catalytic activity of SIR2 for SIR protein spreading in S. cerevisiae. Mol Biol Cell 17: 5287–5297

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  16. Young TJ, Kirchmaier AL (2012) Cell cycle regulation of silent chromatin formation. Biochim Biophys Acta 1819:303–312

    Article  CAS  Google Scholar 

  17. Katan-Khaykovich Y, Struhl K (2005) Heterochromatin formation involves changes in histone modifications over multiple cell generations. EMBO J 24:2138–2149

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  18. Tham WH, Zakian VA (2002) Transcriptional silencing at Saccharomyces telomeres: implications for other organisms. Oncogene 21: 512–521

    Article  PubMed  CAS  Google Scholar 

  19. Jacobi JL, Kirchmaier AL (2011) Propagation of epigenetic states during DNA replication. In: Kusic-Tisma J (ed) Fundamental aspects of DNA replication. In Tech Publishing, Vienna, pp 245–270

    Google Scholar 

  20. Gottschling DE, Aparicio OM, Billington BL et al (1990) Position effect at S. cerevisiae telomeres: reversible repression of Pol II transcription. Cell 63:751–762

    Article  PubMed  CAS  Google Scholar 

  21. Aparicio OM, Billington BL, Gottschling DE (1991) Modifiers of position effect are shared between telomeric and silent mating-type loci in S. cerevisiae. Cell 66:1279–1287

    Article  PubMed  CAS  Google Scholar 

  22. Vega-Palas MA, Martin-Figueroa E, Florencio FJ (2000) Telomeric silencing of a natural subtelomeric gene. Mol Gen Genet 263:287–291

    Article  PubMed  CAS  Google Scholar 

  23. Li C, Mueller JE, Bryk M (2006) Sir2 represses endogenous polymerase II transcription units in the ribosomal DNA nontranscribed spacer. Mol Biol Cell 17:3848–3859

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  24. Yang B, Britton J, Kirchmaier AL (2008) Insights into the impact of histone acetylation and methylation on Sir protein spreading and silencing in Saccharomyces cerevisiae. J Mol Biol 381:826–844

    Article  PubMed  CAS  Google Scholar 

  25. Le S, Davis C, Konopka JB et al (1997) Two new S-phase-specific genes from Saccharomyces cerevisiae. Yeast 13:1029–1042

    Article  PubMed  CAS  Google Scholar 

  26. Axelrod A, Rine J (1991) A role for CDC7 in repression of transcription at the silent mating-type locus HMR in Saccharomyces cerevisiae. Mol Cell Biol 11:1080–1091

    PubMed  CAS  PubMed Central  Google Scholar 

  27. Xu EY, Kim S, Replogle K et al (1999) Identification of SAS4 and SAS5, two genes that regulate silencing in Saccharomyces cerevisiae. Genetics 153:13–23

    PubMed  CAS  PubMed Central  Google Scholar 

  28. Singer MS, Gottschling DE (1994) TLC1: template RNA component of Saccharomyces cerevisiae telomerase. Science 266:404–409

    Article  PubMed  CAS  Google Scholar 

  29. Smith JS, Caputo E, Boeke JD (1999) A genetic screen for ribosomal DNA silencing defects identifies multiple DNA replication and chromatin-modulating factors. Mol Cell Biol 19:3184–3197

    PubMed  CAS  PubMed Central  Google Scholar 

  30. Herskowitz I, Rine J, Strathern J (1992) Mating-type determination and mating-type interconversion in Saccharomyces cerevisiae. In: Jones EW, Pringle JR, Broach JR (eds) The molecular and cellular biology of the yeast Saccharomyces: gene expression. Cold Spring Harbor Laboratory Press, Plainview, NY, pp 583–656

    Google Scholar 

  31. Herskowitz I (1988) Life cycle of the budding yeast Saccharomyces cerevisiae. Microbiol Rev 52:536–553

    PubMed  CAS  PubMed Central  Google Scholar 

  32. Sprague GF Jr, Blair LC, Thorner J (1983) Cell interactions and regulation of cell type in the yeast Saccharomyces cerevisiae. Annu Rev Microbiol 37:623–660

    Article  PubMed  CAS  Google Scholar 

  33. Kimmerly W, Buchman A, Kornberg R et al (1988) Roles of two DNA-binding factors in replication, segregation and transcriptional repression mediated by a yeast silencer. EMBO J 7:2241–2253

    PubMed  CAS  PubMed Central  Google Scholar 

  34. Miller A, Yang B, Foster T et al (2008) Proliferating cell nuclear antigen and ASF1 modulate silent chromatin in Saccharomyces cerevisiae via lysine 56 on histone H3. Genetics 179:793–809

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  35. Ehrenhofer-Murray AE, Kamakaka RT, Rine J (1999) A role for the replication proteins PCNA, RF-C, polymerase ε and Cdc45 in transcriptional silencing in Saccharomyces cerevisiae. Genetics 153:1171–1182

    PubMed  CAS  PubMed Central  Google Scholar 

  36. Miller A, Chen J, Takasuka TE et al (2010) Proliferating cell nuclear antigen (PCNA) is required for cell cycle-regulated silent chromatin on replicated and nonreplicated genes. J Biol Chem 285:35142–35154

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  37. Sprague GF Jr (1991) Assay of yeast mating reaction. Methods Enzymol 194:77–93

    Article  PubMed  CAS  Google Scholar 

  38. Jones EW, Fink GR (1982) Regulation of amino acid and nucleotide biosynthesis in yeast. In: Strathern J, Jones E, Broach JR (eds) The molecular biology of the yeast Saccharomyces: metabolism and gene expression. Cold Spring Harbor Laboratory, Cold Spring Harbor, pp 181–299

    Google Scholar 

  39. Rivier DH, Ekena JL, Rine J (1999) HMR-I is an origin of replication and a silencer in Saccharomyces cerevisiae. Genetics 151:521–529

    PubMed  CAS  PubMed Central  Google Scholar 

  40. Sussel L, Vannier D, Shore D (1993) Epigenetic switching of transcriptional states: cis- and trans-acting factors affecting establishment of silencing at the HMR locus in Saccharomyces cerevisiae. Mol Cell Biol 13:3919–3928

    PubMed  CAS  PubMed Central  Google Scholar 

  41. Yang B, Miller A, Kirchmaier AL (2008) HST3/HST4-dependent deacetylation of lysine 56 of histone H3 in silent chromatin. Mol Biol Cell 19:4993–5005

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  42. Bourns BD, Alexander MK, Smith AM et al (1998) Sir proteins, Rif proteins, and Cdc13p bind Saccharomyces telomeres in vivo. Mol Cell Biol 18:5600–5608

    PubMed  CAS  PubMed Central  Google Scholar 

  43. Miller AM (1984) The yeast MATa1 gene contains two introns. EMBO J 3:1061–1065

    PubMed  CAS  PubMed Central  Google Scholar 

  44. Guthrie C, Fink GR (eds) (2002) Guide to yeast genetics and molecular and cell biology, part B, vol 350, Methods in enzymology. Academic, San Diego, CA, p 623

    Google Scholar 

  45. Sprague GF Jr, Herskowitz I (1981) Control of yeast cell type by the mating type locus. I. Identification and control of expression of the a-specific gene BAR1. J Mol Biol 153:305–321

    Article  PubMed  CAS  Google Scholar 

  46. Adams A, Gottschling DE, Kaiser CA et al (1997) Methods in yeast genetics. In: Dickerson MM (ed) A Cold Spring Harbor laboratory course manual. Cold Spring Harbor Laboratory Press, Plainview, NY, p 177

    Google Scholar 

  47. Hartwell LH (1980) Mutants of Saccharomyces cerevisiae unresponsive to cell division control by polypeptide mating hormone. J Cell Biol 85:811–822

    Article  PubMed  CAS  Google Scholar 

  48. Brachmann CB, Davies A, Cost GJ et al (1998) Designer deletion strains derived from Saccharomyces cerevisiae S288C: a useful set of strains and plasmids for PCR-mediated gene disruption and other applications. Yeast 14: 115–132

    Article  PubMed  CAS  Google Scholar 

  49. Rossmann MP, Luo W, Tsaponina O et al (2011) A common telomeric gene silencing assay is affected by nucleotide metabolism. Mol Cell 42:127–136

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  50. Takahashi YH, Schulze JM, Jackson J et al (2011) Dot1 and histone H3K79 methylation in natural telomeric and HM silencing. Mol Cell 42:118–126

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  51. Schmitt ME, Brown TA, Trumpower BL (1990) A rapid and simple method for preparation of RNA from Saccharomyces cerevisiae. Nucleic Acids Res 18:3091–3092

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  52. Cheng T-H, Gartenberg MR (2000) Yeast heterochromatin is a dynamic structure that requires silencers continuously. Genes Dev 14: 452–463

    PubMed  CAS  PubMed Central  Google Scholar 

  53. Hill JE, Myers AM, Koerner TJ et al (1986) Yeast/E. coli shuttle vectors with multiple unique restriction sites. Yeast 2:163–167

    Article  PubMed  CAS  Google Scholar 

  54. Sherman JM, Stone EM, Freeman-Cook LL et al (1999) The conserved core of a human SIR2 homologue functions in yeast silencing. Mol Biol Cell 10:3045–3059

    Article  PubMed  CAS  PubMed Central  Google Scholar 

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Acknowledgements

This work was supported by the National Science Foundation (A.L.K.) and the Purdue University Center for Cancer Research (A.L.K.).

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Correspondence to Ann L. Kirchmaier .

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Miller, A., Kirchmaier, A.L. (2014). Analysis of Silencing in Saccharomyces cerevisiae . In: Smith, J., Burke, D. (eds) Yeast Genetics. Methods in Molecular Biology, vol 1205. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-1363-3_17

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  • DOI: https://doi.org/10.1007/978-1-4939-1363-3_17

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  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-1362-6

  • Online ISBN: 978-1-4939-1363-3

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