Skip to main content
Genetics logoLink to Genetics
. 1998 Oct;150(2):563–576. doi: 10.1093/genetics/150.2.563

Histone deacetylase homologs regulate epigenetic inheritance of transcriptional silencing and chromosome segregation in fission yeast.

S I Grewal 1, M J Bonaduce 1, A J Klar 1
PMCID: PMC1460350  PMID: 9755190

Abstract

Position-effect control at the silent mat2-mat3 interval and at centromeres and telomeres in fission yeast is suggested to be mediated through the assembly of heterochromatin-like structures. Therefore, trans-acting genes that affect silencing may encode either chromatin proteins, factors that modify them, or factors that affect chromatin assembly. Here, we report the identification of an essential gene, clr6 (cryptic loci regulator), which encodes a putative histone deacetylase that when mutated affects epigenetically maintained repression at the mat2-mat3 region and at centromeres and reduces the fidelity of chromosome segregation. Furthermore, we show that the Clr3 protein, when mutated, alleviates recombination block at mat region as well as silencing at donor loci and at centromeres and telomeres, also shares strong homology to known histone deacetylases. Genetic analyses indicate that silencing might be regulated by at least two overlapping histone deacetylase activities. We also found that transient inhibition of histone deacetylase activity by trichostatin A results in the increased missegregation of chromosomes in subsequent generations and, remarkably, alters the imprint at the mat locus, causing the heritable conversion of the repressed epigenetic state to the expressed state. This work supports the model that the level of histone deacetylation has a role in the assembly of repressive heterochromatin and provides insight into the mechanism of epigenetic inheritance.

Full Text

The Full Text of this article is available as a PDF (506.2 KB).

Selected References

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

  1. Allshire R. C., Nimmo E. R., Ekwall K., Javerzat J. P., Cranston G. Mutations derepressing silent centromeric domains in fission yeast disrupt chromosome segregation. Genes Dev. 1995 Jan 15;9(2):218–233. doi: 10.1101/gad.9.2.218. [DOI] [PubMed] [Google Scholar]
  2. Arcangioli B., Klar A. J. A novel switch-activating site (SAS1) and its cognate binding factor (SAP1) required for efficient mat1 switching in Schizosaccharomyces pombe. EMBO J. 1991 Oct;10(10):3025–3032. doi: 10.1002/j.1460-2075.1991.tb07853.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Barlow D. P. Gametic imprinting in mammals. Science. 1995 Dec 8;270(5242):1610–1613. doi: 10.1126/science.270.5242.1610. [DOI] [PubMed] [Google Scholar]
  4. Braunstein M., Rose A. B., Holmes S. G., Allis C. D., Broach J. R. Transcriptional silencing in yeast is associated with reduced nucleosome acetylation. Genes Dev. 1993 Apr;7(4):592–604. doi: 10.1101/gad.7.4.592. [DOI] [PubMed] [Google Scholar]
  5. Bresch C., Müller G., Egel R. Genes involved in meiosis and sporulation of a yeast. Mol Gen Genet. 1968;102(4):301–306. doi: 10.1007/BF00433721. [DOI] [PubMed] [Google Scholar]
  6. Brownell J. E., Allis C. D. Special HATs for special occasions: linking histone acetylation to chromatin assembly and gene activation. Curr Opin Genet Dev. 1996 Apr;6(2):176–184. doi: 10.1016/s0959-437x(96)80048-7. [DOI] [PubMed] [Google Scholar]
  7. Buck S. W., Shore D. Action of a RAP1 carboxy-terminal silencing domain reveals an underlying competition between HMR and telomeres in yeast. Genes Dev. 1995 Feb 1;9(3):370–384. doi: 10.1101/gad.9.3.370. [DOI] [PubMed] [Google Scholar]
  8. Clarke L., Baum M., Marschall L. G., Ngan V. K., Steiner N. C. Structure and function of Schizosaccharomyces pombe centromeres. Cold Spring Harb Symp Quant Biol. 1993;58:687–695. doi: 10.1101/sqb.1993.058.01.076. [DOI] [PubMed] [Google Scholar]
  9. De Rubertis F., Kadosh D., Henchoz S., Pauli D., Reuter G., Struhl K., Spierer P. The histone deacetylase RPD3 counteracts genomic silencing in Drosophila and yeast. Nature. 1996 Dec 12;384(6609):589–591. doi: 10.1038/384589a0. [DOI] [PubMed] [Google Scholar]
  10. Ekwall K., Javerzat J. P., Lorentz A., Schmidt H., Cranston G., Allshire R. The chromodomain protein Swi6: a key component at fission yeast centromeres. Science. 1995 Sep 8;269(5229):1429–1431. doi: 10.1126/science.7660126. [DOI] [PubMed] [Google Scholar]
  11. Ekwall K., Olsson T., Turner B. M., Cranston G., Allshire R. C. Transient inhibition of histone deacetylation alters the structural and functional imprint at fission yeast centromeres. Cell. 1997 Dec 26;91(7):1021–1032. doi: 10.1016/s0092-8674(00)80492-4. [DOI] [PubMed] [Google Scholar]
  12. Ekwall K., Ruusala T. Mutations in rik1, clr2, clr3 and clr4 genes asymmetrically derepress the silent mating-type loci in fission yeast. Genetics. 1994 Jan;136(1):53–64. doi: 10.1093/genetics/136.1.53. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. Gottschling D. E., Aparicio O. M., Billington B. L., Zakian V. A. Position effect at S. cerevisiae telomeres: reversible repression of Pol II transcription. Cell. 1990 Nov 16;63(4):751–762. doi: 10.1016/0092-8674(90)90141-z. [DOI] [PubMed] [Google Scholar]
  14. Grewal S. I., Klar A. J. A recombinationally repressed region between mat2 and mat3 loci shares homology to centromeric repeats and regulates directionality of mating-type switching in fission yeast. Genetics. 1997 Aug;146(4):1221–1238. doi: 10.1093/genetics/146.4.1221. [DOI] [PMC free article] [PubMed] [Google Scholar]
  15. Grewal S. I., Klar A. J. Chromosomal inheritance of epigenetic states in fission yeast during mitosis and meiosis. Cell. 1996 Jul 12;86(1):95–101. doi: 10.1016/s0092-8674(00)80080-x. [DOI] [PubMed] [Google Scholar]
  16. Hartzog G. A., Winston F. Nucleosomes and transcription: recent lessons from genetics. Curr Opin Genet Dev. 1997 Apr;7(2):192–198. doi: 10.1016/s0959-437x(97)80128-1. [DOI] [PubMed] [Google Scholar]
  17. Hoheisel J. D., Maier E., Mott R., McCarthy L., Grigoriev A. V., Schalkwyk L. C., Nizetic D., Francis F., Lehrach H. High resolution cosmid and P1 maps spanning the 14 Mb genome of the fission yeast S. pombe. Cell. 1993 Apr 9;73(1):109–120. doi: 10.1016/0092-8674(93)90164-l. [DOI] [PubMed] [Google Scholar]
  18. Ivanova A. V., Bonaduce M. J., Ivanov S. V., Klar A. J. The chromo and SET domains of the Clr4 protein are essential for silencing in fission yeast. Nat Genet. 1998 Jun;19(2):192–195. doi: 10.1038/566. [DOI] [PubMed] [Google Scholar]
  19. Klar A. J., Ivanova A. V., Dalgaard J. Z., Bonaduce M. J., Grewal S. I. Multiple epigenetic events regulate mating-type switching of fission yeast. Novartis Found Symp. 1998;214:87–103. doi: 10.1002/9780470515501.ch6. [DOI] [PubMed] [Google Scholar]
  20. Lorentz A., Heim L., Schmidt H. The switching gene swi6 affects recombination and gene expression in the mating-type region of Schizosaccharomyces pombe. Mol Gen Genet. 1992 Jun;233(3):436–442. doi: 10.1007/BF00265441. [DOI] [PubMed] [Google Scholar]
  21. Lorentz A., Ostermann K., Fleck O., Schmidt H. Switching gene swi6, involved in repression of silent mating-type loci in fission yeast, encodes a homologue of chromatin-associated proteins from Drosophila and mammals. Gene. 1994 May 27;143(1):139–143. doi: 10.1016/0378-1119(94)90619-x. [DOI] [PubMed] [Google Scholar]
  22. Maillet L., Boscheron C., Gotta M., Marcand S., Gilson E., Gasser S. M. Evidence for silencing compartments within the yeast nucleus: a role for telomere proximity and Sir protein concentration in silencer-mediated repression. Genes Dev. 1996 Jul 15;10(14):1796–1811. doi: 10.1101/gad.10.14.1796. [DOI] [PubMed] [Google Scholar]
  23. Orlando V., Paro R. Chromatin multiprotein complexes involved in the maintenance of transcription patterns. Curr Opin Genet Dev. 1995 Apr;5(2):174–179. doi: 10.1016/0959-437x(95)80005-0. [DOI] [PubMed] [Google Scholar]
  24. Paro R. Mechanisms of heritable gene repression during development of Drosophila. Curr Opin Cell Biol. 1993 Dec;5(6):999–1005. doi: 10.1016/0955-0674(93)90084-4. [DOI] [PubMed] [Google Scholar]
  25. Polizzi C., Clarke L. The chromatin structure of centromeres from fission yeast: differentiation of the central core that correlates with function. J Cell Biol. 1991 Jan;112(2):191–201. doi: 10.1083/jcb.112.2.191. [DOI] [PMC free article] [PubMed] [Google Scholar]
  26. Reynolds P., Koken M. H., Hoeijmakers J. H., Prakash S., Prakash L. The rhp6+ gene of Schizosaccharomyces pombe: a structural and functional homolog of the RAD6 gene from the distantly related yeast Saccharomyces cerevisiae. EMBO J. 1990 May;9(5):1423–1430. doi: 10.1002/j.1460-2075.1990.tb08258.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  27. Rundlett S. E., Carmen A. A., Kobayashi R., Bavykin S., Turner B. M., Grunstein M. HDA1 and RPD3 are members of distinct yeast histone deacetylase complexes that regulate silencing and transcription. Proc Natl Acad Sci U S A. 1996 Dec 10;93(25):14503–14508. doi: 10.1073/pnas.93.25.14503. [DOI] [PMC free article] [PubMed] [Google Scholar]
  28. Schmitt M. E., Brown T. A., Trumpower B. L. A rapid and simple method for preparation of RNA from Saccharomyces cerevisiae. Nucleic Acids Res. 1990 May 25;18(10):3091–3092. doi: 10.1093/nar/18.10.3091. [DOI] [PMC free article] [PubMed] [Google Scholar]
  29. Takahashi K., Murakami S., Chikashige Y., Funabiki H., Niwa O., Yanagida M. A low copy number central sequence with strict symmetry and unusual chromatin structure in fission yeast centromere. Mol Biol Cell. 1992 Jul;3(7):819–835. doi: 10.1091/mbc.3.7.819. [DOI] [PMC free article] [PubMed] [Google Scholar]
  30. Taunton J., Hassig C. A., Schreiber S. L. A mammalian histone deacetylase related to the yeast transcriptional regulator Rpd3p. Science. 1996 Apr 19;272(5260):408–411. doi: 10.1126/science.272.5260.408. [DOI] [PubMed] [Google Scholar]
  31. Thon G., Cohen A., Klar A. J. Three additional linkage groups that repress transcription and meiotic recombination in the mating-type region of Schizosaccharomyces pombe. Genetics. 1994 Sep;138(1):29–38. doi: 10.1093/genetics/138.1.29. [DOI] [PMC free article] [PubMed] [Google Scholar]
  32. Thon G., Friis T. Epigenetic inheritance of transcriptional silencing and switching competence in fission yeast. Genetics. 1997 Mar;145(3):685–696. doi: 10.1093/genetics/145.3.685. [DOI] [PMC free article] [PubMed] [Google Scholar]
  33. Thon G., Klar A. J. The clr1 locus regulates the expression of the cryptic mating-type loci of fission yeast. Genetics. 1992 Jun;131(2):287–296. doi: 10.1093/genetics/131.2.287. [DOI] [PMC free article] [PubMed] [Google Scholar]
  34. Vannier D., Balderes D., Shore D. Evidence that the transcriptional regulators SIN3 and RPD3, and a novel gene (SDS3) with similar functions, are involved in transcriptional silencing in S. cerevisiae. Genetics. 1996 Dec;144(4):1343–1353. doi: 10.1093/genetics/144.4.1343. [DOI] [PMC free article] [PubMed] [Google Scholar]
  35. Vidal M., Gaber R. F. RPD3 encodes a second factor required to achieve maximum positive and negative transcriptional states in Saccharomyces cerevisiae. Mol Cell Biol. 1991 Dec;11(12):6317–6327. doi: 10.1128/mcb.11.12.6317. [DOI] [PMC free article] [PubMed] [Google Scholar]
  36. Yoshida M., Horinouchi S., Beppu T. Trichostatin A and trapoxin: novel chemical probes for the role of histone acetylation in chromatin structure and function. Bioessays. 1995 May;17(5):423–430. doi: 10.1002/bies.950170510. [DOI] [PubMed] [Google Scholar]

Articles from Genetics are provided here courtesy of Oxford University Press

RESOURCES