Skip to main content
PMC home page
The EMBO Journal logoLink to The EMBO Journal
. 1997 Jun 2;16(11):3243–3255. doi: 10.1093/emboj/16.11.3243

Localization of Sir2p: the nucleolus as a compartment for silent information regulators.

M Gotta 1, S Strahl-Bolsinger 1, H Renauld 1, T Laroche 1, B K Kennedy 1, M Grunstein 1, S M Gasser 1
PMCID: PMC1169941  PMID: 9214640

Abstract

In wild-type budding yeast strains, the proteins encoded by SIR3, SIR4 and RAP1 co-localize with telomeric DNA in a limited number of foci in interphase nuclei. Immunostaining of Sir2p shows that in addition to a punctate staining that coincides with Rap1 foci, Sir2p localizes to a subdomain of the nucleolus. The presence of Sir2p at both the spacer of the rDNA repeat and at telomeres is confirmed by formaldehyde cross-linking and immunoprecipitation with anti-Sir2p antibodies. In strains lacking Sir4p, Sir3p becomes concentrated in the nucleolus, by a pathway requiring SIR2 and UTH4, a gene that regulates life span in yeast. The unexpected nucleolar localization of Sir2p and Sir3p correlates with observed effects of sir mutations on rDNA stability and yeast longevity, defining a new site of action for silent information regulatory factors.

Full Text

The Full Text of this article is available as a PDF (348.4 KB).

Selected References

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

  1. Aparicio O. M., Billington B. L., Gottschling D. E. Modifiers of position effect are shared between telomeric and silent mating-type loci in S. cerevisiae. Cell. 1991 Sep 20;66(6):1279–1287. doi: 10.1016/0092-8674(91)90049-5. [DOI] [PubMed] [Google Scholar]
  2. Aris J. P., Blobel G. Identification and characterization of a yeast nucleolar protein that is similar to a rat liver nucleolar protein. J Cell Biol. 1988 Jul;107(1):17–31. doi: 10.1083/jcb.107.1.17. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Brachmann C. B., Sherman J. M., Devine S. E., Cameron E. E., Pillus L., Boeke J. D. The SIR2 gene family, conserved from bacteria to humans, functions in silencing, cell cycle progression, and chromosome stability. Genes Dev. 1995 Dec 1;9(23):2888–2902. doi: 10.1101/gad.9.23.2888. [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. Bryk M., Banerjee M., Murphy M., Knudsen K. E., Garfinkel D. J., Curcio M. J. Transcriptional silencing of Ty1 elements in the RDN1 locus of yeast. Genes Dev. 1997 Jan 15;11(2):255–269. doi: 10.1101/gad.11.2.255. [DOI] [PubMed] [Google Scholar]
  6. Buchman A. R., Kimmerly W. J., Rine J., Kornberg R. D. Two DNA-binding factors recognize specific sequences at silencers, upstream activating sequences, autonomously replicating sequences, and telomeres in Saccharomyces cerevisiae. Mol Cell Biol. 1988 Jan;8(1):210–225. doi: 10.1128/mcb.8.1.210. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. Cockell M., Palladino F., Laroche T., Kyrion G., Liu C., Lustig A. J., Gasser S. M. The carboxy termini of Sir4 and Rap1 affect Sir3 localization: evidence for a multicomponent complex required for yeast telomeric silencing. J Cell Biol. 1995 May;129(4):909–924. doi: 10.1083/jcb.129.4.909. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Derbyshire M. K., Weinstock K. G., Strathern J. N. HST1, a new member of the SIR2 family of genes. Yeast. 1996 Jun 15;12(7):631–640. doi: 10.1002/(SICI)1097-0061(19960615)12:7%3C631::AID-YEA960%3E3.0.CO;2-8. [DOI] [PubMed] [Google Scholar]
  9. Dorer D. R., Henikoff S. Expansions of transgene repeats cause heterochromatin formation and gene silencing in Drosophila. Cell. 1994 Jul 1;77(7):993–1002. doi: 10.1016/0092-8674(94)90439-1. [DOI] [PubMed] [Google Scholar]
  10. Fogel S., Welch J. W. Tandem gene amplification mediates copper resistance in yeast. Proc Natl Acad Sci U S A. 1982 Sep;79(17):5342–5346. doi: 10.1073/pnas.79.17.5342. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. Foss M., McNally F. J., Laurenson P., Rine J. Origin recognition complex (ORC) in transcriptional silencing and DNA replication in S. cerevisiae. Science. 1993 Dec 17;262(5141):1838–1844. doi: 10.1126/science.8266071. [DOI] [PubMed] [Google Scholar]
  12. Gotta M., Gasser S. M. Nuclear organization and transcriptional silencing in yeast. Experientia. 1996 Dec 15;52(12):1136–1147. doi: 10.1007/BF01952113. [DOI] [PubMed] [Google Scholar]
  13. Gotta M., Laroche T., Formenton A., Maillet L., Scherthan H., Gasser S. M. The clustering of telomeres and colocalization with Rap1, Sir3, and Sir4 proteins in wild-type Saccharomyces cerevisiae. J Cell Biol. 1996 Sep;134(6):1349–1363. doi: 10.1083/jcb.134.6.1349. [DOI] [PMC free article] [PubMed] [Google Scholar]
  14. Gottlieb S., Esposito R. E. A new role for a yeast transcriptional silencer gene, SIR2, in regulation of recombination in ribosomal DNA. Cell. 1989 Mar 10;56(5):771–776. doi: 10.1016/0092-8674(89)90681-8. [DOI] [PubMed] [Google Scholar]
  15. Guacci V., Hogan E., Koshland D. Chromosome condensation and sister chromatid pairing in budding yeast. J Cell Biol. 1994 May;125(3):517–530. doi: 10.1083/jcb.125.3.517. [DOI] [PMC free article] [PubMed] [Google Scholar]
  16. Hecht A., Laroche T., Strahl-Bolsinger S., Gasser S. M., Grunstein M. Histone H3 and H4 N-termini interact with SIR3 and SIR4 proteins: a molecular model for the formation of heterochromatin in yeast. Cell. 1995 Feb 24;80(4):583–592. doi: 10.1016/0092-8674(95)90512-x. [DOI] [PubMed] [Google Scholar]
  17. Hecht A., Strahl-Bolsinger S., Grunstein M. Spreading of transcriptional repressor SIR3 from telomeric heterochromatin. Nature. 1996 Sep 5;383(6595):92–96. doi: 10.1038/383092a0. [DOI] [PubMed] [Google Scholar]
  18. Henikoff S. Position effect and related phenomena. Curr Opin Genet Dev. 1992 Dec;2(6):907–912. doi: 10.1016/s0959-437x(05)80114-5. [DOI] [PubMed] [Google Scholar]
  19. Hilliker A. J., Appels R., Schalet A. The genetic analysis of D. melanogaster heterochromatin. Cell. 1980 Oct;21(3):607–619. doi: 10.1016/0092-8674(80)90424-9. [DOI] [PubMed] [Google Scholar]
  20. Ivy J. M., Klar A. J., Hicks J. B. Cloning and characterization of four SIR genes of Saccharomyces cerevisiae. Mol Cell Biol. 1986 Feb;6(2):688–702. doi: 10.1128/mcb.6.2.688. [DOI] [PMC free article] [PubMed] [Google Scholar]
  21. Ju Q. D., Morrow B. E., Warner J. R. REB1, a yeast DNA-binding protein with many targets, is essential for growth and bears some resemblance to the oncogene myb. Mol Cell Biol. 1990 Oct;10(10):5226–5234. doi: 10.1128/mcb.10.10.5226. [DOI] [PMC free article] [PubMed] [Google Scholar]
  22. Kayne P. S., Kim U. J., Han M., Mullen J. R., Yoshizaki F., Grunstein M. Extremely conserved histone H4 N terminus is dispensable for growth but essential for repressing the silent mating loci in yeast. Cell. 1988 Oct 7;55(1):27–39. doi: 10.1016/0092-8674(88)90006-2. [DOI] [PubMed] [Google Scholar]
  23. Kennedy B. K., Austriaco N. R., Jr, Zhang J., Guarente L. Mutation in the silencing gene SIR4 can delay aging in S. cerevisiae. Cell. 1995 Feb 10;80(3):485–496. doi: 10.1016/0092-8674(95)90499-9. [DOI] [PubMed] [Google Scholar]
  24. Klein F., Laroche T., Cardenas M. E., Hofmann J. F., Schweizer D., Gasser S. M. Localization of RAP1 and topoisomerase II in nuclei and meiotic chromosomes of yeast. J Cell Biol. 1992 Jun;117(5):935–948. doi: 10.1083/jcb.117.5.935. [DOI] [PMC free article] [PubMed] [Google Scholar]
  25. Kyrion G., Liu K., Liu C., Lustig A. J. RAP1 and telomere structure regulate telomere position effects in Saccharomyces cerevisiae. Genes Dev. 1993 Jul;7(7A):1146–1159. doi: 10.1101/gad.7.7a.1146. [DOI] [PubMed] [Google Scholar]
  26. Liu C., Mao X., Lustig A. J. Mutational analysis defines a C-terminal tail domain of RAP1 essential for Telomeric silencing in Saccharomyces cerevisiae. Genetics. 1994 Dec;138(4):1025–1040. doi: 10.1093/genetics/138.4.1025. [DOI] [PMC free article] [PubMed] [Google Scholar]
  27. 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]
  28. Marcand S., Buck S. W., Moretti P., Gilson E., Shore D. Silencing of genes at nontelomeric sites in yeast is controlled by sequestration of silencing factors at telomeres by Rap 1 protein. Genes Dev. 1996 Jun 1;10(11):1297–1309. doi: 10.1101/gad.10.11.1297. [DOI] [PubMed] [Google Scholar]
  29. Marcand S., Gasser S. M., Gilson E. Chromatin: a sticky silence. Curr Biol. 1996 Oct 1;6(10):1222–1225. doi: 10.1016/s0960-9822(96)00701-4. [DOI] [PubMed] [Google Scholar]
  30. McKee B. D., Karpen G. H. Drosophila ribosomal RNA genes function as an X-Y pairing site during male meiosis. Cell. 1990 Apr 6;61(1):61–72. doi: 10.1016/0092-8674(90)90215-z. [DOI] [PubMed] [Google Scholar]
  31. Moazed D., Johnson D. A deubiquitinating enzyme interacts with SIR4 and regulates silencing in S. cerevisiae. Cell. 1996 Aug 23;86(4):667–677. doi: 10.1016/s0092-8674(00)80139-7. [DOI] [PubMed] [Google Scholar]
  32. Moretti P., Freeman K., Coodly L., Shore D. Evidence that a complex of SIR proteins interacts with the silencer and telomere-binding protein RAP1. Genes Dev. 1994 Oct 1;8(19):2257–2269. doi: 10.1101/gad.8.19.2257. [DOI] [PubMed] [Google Scholar]
  33. Orlando V., Paro R. Mapping Polycomb-repressed domains in the bithorax complex using in vivo formaldehyde cross-linked chromatin. Cell. 1993 Dec 17;75(6):1187–1198. doi: 10.1016/0092-8674(93)90328-n. [DOI] [PubMed] [Google Scholar]
  34. Palladino F., Laroche T., Gilson E., Axelrod A., Pillus L., Gasser S. M. SIR3 and SIR4 proteins are required for the positioning and integrity of yeast telomeres. Cell. 1993 Nov 5;75(3):543–555. doi: 10.1016/0092-8674(93)90388-7. [DOI] [PubMed] [Google Scholar]
  35. Palladino F., Laroche T., Gilson E., Pillus L., Gasser S. M. The positioning of yeast telomeres depends on SIR3, SIR4, and the integrity of the nuclear membrane. Cold Spring Harb Symp Quant Biol. 1993;58:733–746. doi: 10.1101/sqb.1993.058.01.081. [DOI] [PubMed] [Google Scholar]
  36. Peter M., Neiman A. M., Park H. O., van Lohuizen M., Herskowitz I. Functional analysis of the interaction between the small GTP binding protein Cdc42 and the Ste20 protein kinase in yeast. EMBO J. 1996 Dec 16;15(24):7046–7059. [PMC free article] [PubMed] [Google Scholar]
  37. Renauld H., Aparicio O. M., Zierath P. D., Billington B. L., Chhablani S. K., Gottschling D. E. Silent domains are assembled continuously from the telomere and are defined by promoter distance and strength, and by SIR3 dosage. Genes Dev. 1993 Jul;7(7A):1133–1145. doi: 10.1101/gad.7.7a.1133. [DOI] [PubMed] [Google Scholar]
  38. Renauld H. Heterochromatin: a meiotic matchmaker? Trends Cell Biol. 1997 May;7(5):201–205. doi: 10.1016/S0962-8924(97)01034-9. [DOI] [PubMed] [Google Scholar]
  39. Rine J., Herskowitz I. Four genes responsible for a position effect on expression from HML and HMR in Saccharomyces cerevisiae. Genetics. 1987 May;116(1):9–22. doi: 10.1093/genetics/116.1.9. [DOI] [PMC free article] [PubMed] [Google Scholar]
  40. Rossignol J. L., Faugeron G. MIP: an epigenetic gene silencing process in Ascobolus immersus. Curr Top Microbiol Immunol. 1995;197:179–191. doi: 10.1007/978-3-642-79145-1_12. [DOI] [PubMed] [Google Scholar]
  41. Sabl J. F., Henikoff S. Copy number and orientation determine the susceptibility of a gene to silencing by nearby heterochromatin in Drosophila. Genetics. 1996 Feb;142(2):447–458. doi: 10.1093/genetics/142.2.447. [DOI] [PMC free article] [PubMed] [Google Scholar]
  42. Sandell L. L., Zakian V. A. Telomeric position effect in yeast. Trends Cell Biol. 1992 Jan;2(1):10–14. doi: 10.1016/0962-8924(92)90138-d. [DOI] [PubMed] [Google Scholar]
  43. Scheer U., Weisenberger D. The nucleolus. Curr Opin Cell Biol. 1994 Jun;6(3):354–359. doi: 10.1016/0955-0674(94)90026-4. [DOI] [PubMed] [Google Scholar]
  44. Smith J. S., Boeke J. D. An unusual form of transcriptional silencing in yeast ribosomal DNA. Genes Dev. 1997 Jan 15;11(2):241–254. doi: 10.1101/gad.11.2.241. [DOI] [PubMed] [Google Scholar]
  45. Solomon M. J., Larsen P. L., Varshavsky A. Mapping protein-DNA interactions in vivo with formaldehyde: evidence that histone H4 is retained on a highly transcribed gene. Cell. 1988 Jun 17;53(6):937–947. doi: 10.1016/s0092-8674(88)90469-2. [DOI] [PubMed] [Google Scholar]
  46. Stewart S. E., Roeder G. S. Transcription by RNA polymerase I stimulates mitotic recombination in Saccharomyces cerevisiae. Mol Cell Biol. 1989 Aug;9(8):3464–3472. doi: 10.1128/mcb.9.8.3464. [DOI] [PMC free article] [PubMed] [Google Scholar]
  47. Stone E. M., Swanson M. J., Romeo A. M., Hicks J. B., Sternglanz R. The SIR1 gene of Saccharomyces cerevisiae and its role as an extragenic suppressor of several mating-defective mutants. Mol Cell Biol. 1991 Apr;11(4):2253–2262. doi: 10.1128/mcb.11.4.2253. [DOI] [PMC free article] [PubMed] [Google Scholar]
  48. Sussel L., Shore D. Separation of transcriptional activation and silencing functions of the RAP1-encoded repressor/activator protein 1: isolation of viable mutants affecting both silencing and telomere length. Proc Natl Acad Sci U S A. 1991 Sep 1;88(17):7749–7753. doi: 10.1073/pnas.88.17.7749. [DOI] [PMC free article] [PubMed] [Google Scholar]
  49. Thompson J. S., Hecht A., Grunstein M. Histones and the regulation of heterochromatin in yeast. Cold Spring Harb Symp Quant Biol. 1993;58:247–256. doi: 10.1101/sqb.1993.058.01.029. [DOI] [PubMed] [Google Scholar]
  50. Tollervey D., Lehtonen H., Jansen R., Kern H., Hurt E. C. Temperature-sensitive mutations demonstrate roles for yeast fibrillarin in pre-rRNA processing, pre-rRNA methylation, and ribosome assembly. Cell. 1993 Feb 12;72(3):443–457. doi: 10.1016/0092-8674(93)90120-f. [DOI] [PubMed] [Google Scholar]
  51. Uzawa S., Yanagida M. Visualization of centromeric and nucleolar DNA in fission yeast by fluorescence in situ hybridization. J Cell Sci. 1992 Feb;101(Pt 2):267–275. doi: 10.1242/jcs.101.2.267. [DOI] [PubMed] [Google Scholar]

Articles from The EMBO Journal are provided here courtesy of Nature Publishing Group

RESOURCES