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Nuclear architecture and spatial positioning help establish transcriptional states of telomeres in yeast

Nature Cell Biology volume 4, pages 214–221 (2002)Cite this article

Abstract

Recent experiments have shown that gene repression can be correlated with relocation of genes to heterochromatin-rich silent domains. Here, we investigate whether nuclear architecture and spatial positioning can contribute directly to the transcriptional activity of a genetic locus in Saccharomyces cerevisiae. By disassembling telomeric silent domains without altering the chromatin-mediated silencing machinery, we show that the transcriptional activity of silencer–reporter constructs depends on intranuclear position. This demonstrates that telomeric silent domains are actively involved in transcriptional silencing. Employing fluorescent in situ hybridization (FISH) in combination with genetic assays, we demonstrate that telomeres control the establishment of transcriptional states by reversible partitioning with the perinuclear silencing domains. Anchoring telomeres interferes with their ability to assume an active state, whereas disassembly of silencing domains prevents telomeres from assuming a repressed state. Our data support a model in which domains of enriched transcriptional regulators allow genes to determine transcriptional states by spatial positioning.

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Figure 1: Nup60p links the NPC-core component Nup145p with intranuclear Mlp-extensions.
Figure 2: Deletion of the C-terminal part of Nup145p, NUP60 or MLP2 release telomeres from their perinuclear localization.
Figure 3: Dismantling silent domains abolishes perinuclear-dependent silencing.
Figure 4: Deletion of structural components of the silent domain leads to an increase in ectopic silencing and a concomitant release of silencing factors from their perinuclear localization.
Figure 5: Repression of a subtelomeric reporter leads to its relocation into telomeric clusters.
Figure 6: Anchoring a subtelomeric reporter gene into intact silent domains prevents it from reassuming an active state.
Figure 7: The integrity of silent domains is required for the effective establishment of transcriptional states.

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References

  1. Dernburg, A. F. et al. Perturbation of nuclear architecture by long-distance chromosome interactions. Cell 85, 745–759 (1996).

    Article  CAS  PubMed  Google Scholar 

  2. Gerasimova, T. I., Byrd, K. & Corces, V. G. A chromatin insulator determines the nuclear localization of DNA. Mol. Cell 6, 1025–1035 (2000).

    Article  CAS  PubMed  Google Scholar 

  3. Brown, K. E. et al. Association of transcriptionally silent genes with Ikaros complexes at centromeric heterochromatin. Cell 91, 845–854 (1997).

    Article  CAS  PubMed  Google Scholar 

  4. Brown, K. E., Baxter, J., Graf, D., Merkenschlager, M. & Fisher, A. G. Dynamic repositioning of genes in the nucleus of lymphocytes preparing for cell division. Mol. Cell 3, 207–217 (1999).

    Article  CAS  PubMed  Google Scholar 

  5. Francastel, C., Walters, M. C., Groudine, M. & Martin, D. I. A functional enhancer suppresses silencing of a transgene and prevents its localization close to centrometric heterochromatin. Cell 99, 259–269 (1999).

    Article  CAS  PubMed  Google Scholar 

  6. Cockell, M. & Gasser, S. M. Nuclear compartments and gene regulation. Curr. Opin. Genet. Dev. 9, 199–205 (1999).

    Article  CAS  PubMed  Google Scholar 

  7. Cooper, J. P. Telomere transitions in yeast: the end of the chromosome as we know it. Curr. Opin. Genet. Dev. 10, 169–177 (2000).

    Article  CAS  PubMed  Google Scholar 

  8. Andrulis, E. D., Neiman, A. M., Zappulla, D. C. & Sternglanz, R. Perinuclear localization of chromatin facilitates transcriptional silencing. Nature 394, 592–595 (1998); Erratum, Nature 395, 525 (1998).

    Article  CAS  PubMed  Google Scholar 

  9. Maillet, L. et al. Evidence for silencing compartments within the yeast nucleus: a role for telomere proximity and Sir protein concentration in silencer-mediated repression. Genes Dev. 10, 1796–1811 (1996).

    Article  CAS  PubMed  Google Scholar 

  10. Galy, V. et al. Nuclear pore complexes in the organization of silent telomeric chromatin. Nature 403, 108–112 (2000).

    Article  CAS  PubMed  Google Scholar 

  11. Rout, M. P. et al. The yeast nuclear pore complex: composition, architecture, and transport mechanism. J. Cell Biol. 148, 635–651 (2000).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  12. Fromont-Racine, M., Rain, J. C. & Legrain, P. Toward a functional analysis of the yeast genome through exhaustive two-hybrid screens. Nature Genet. 16, 277–282 (1997).

    Article  CAS  PubMed  Google Scholar 

  13. Gotta, M. et al. The clustering of telomeres and colocalization with Rap1, Sir3, and Sir4 proteins in wild-type Saccharomyces cerevisiae. J. Cell Biol. 134, 1349–1363 (1996).

    Article  CAS  PubMed  Google Scholar 

  14. Maillet, L. et al. Ku-deficient yeast strains exhibit alternative states of silencing competence. EMBO Rep. 2, 203–210 (2001).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  15. Laroche, T. et al. Mutation of yeast Ku genes disrupts the subnuclear organization of telomeres. Curr. Biol. 8, 653–656 (1998).

    Article  CAS  PubMed  Google Scholar 

  16. 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 63, 751–762 (1990).

    Article  CAS  PubMed  Google Scholar 

  17. Khosravi-Far, R. et al. Isoprenoid modification of rab proteins terminating in CC or CXC motifs. Proc. Natl Acad. Sci. USA 88, 6264–6268 (1991).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  18. Kinsella, B. T. & Maltese, W. A. rab GTP-binding proteins with three different carboxyl-terminal cysteine motifs are modified in vivo by 20-carbon isoprenoids. J. Biol. Chem. 267, 3940–3945 (1992).

    CAS  PubMed  Google Scholar 

  19. Tham, W., Wyithe, J. S., Ferrigno, P. K., Silver, P. A. & Zakian, V. A. Localization of yeast telomeres to the nuclear periphery is separable from transcriptional repression and telomere stability functions. Mol. Cell 8, 189–199 (2001).

    Article  CAS  PubMed  Google Scholar 

  20. Aparicio, O. M. & Gottschling, D. E. Overcoming telomeric silencing: a trans-activator competes to establish gene expression in a cell cycle-dependent way. Genes Dev. 8, 1133–1146 (1994).

    Article  CAS  PubMed  Google Scholar 

  21. Kosova, B. et al. Mlp2p, a component of nuclear pore attached intranuclear filaments, associates with nic96p. J. Biol. Chem. 275, 343–350 (2000).

    Article  CAS  PubMed  Google Scholar 

  22. Strambio-de-Castillia, C., Blobel, G. & Rout, M. P. Proteins connecting the nuclear pore complex with the nuclear interior. J. Cell Biol. 144, 839–855 (1999).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  23. Brown, K. E. et al. Expression of alpha- and beta-globin genes occurs within different nuclear domains in haemopoietic cells. Nature Cell Biol. 3, 602–606 (2001).

    Article  CAS  PubMed  Google Scholar 

  24. Francastel, C., Schubeler, D., Martin, D. I. & Groudine, M. Nuclear compartmentalization and gene activity. Nature Rev. Mol. Cell Biol. 1, 137–143 (2000).

    Article  CAS  Google Scholar 

  25. Skok, J. A. et al. Nonequivalent nuclear location of immunoglobulin alleles in B lymphocytes. Nature Immunol. 2, 848–854 (2001).

    Article  CAS  Google Scholar 

  26. Rose, M. D., Winston, F. & Hieter, P. Methods in Yeast Genetics. A Laboratory Manual (Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY, 1990).

  27. Boeke, J. D., LaCroute, F. & Fink, G. R. A positive selection for mutants lacking orotidine-5′-phosphate decarboxylase activity in yeast: 5-fluoro-orotic acid resistance. Mol. Gen. Genet. 197, 345–346 (1984).

    Article  CAS  PubMed  Google Scholar 

  28. Baudin, A., Ozier-Kalogeropoulos, O., Denouel, A., Lacroute, F. & Cullin, C. A simple and efficient method for direct gene deletion in Saccharomyces cerevisiae. Nucleic Acids Res. 21, 3329–3330 (1993).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  29. Fourel, G., Revardel, E., Koering, C. E. & Gilson, E. Cohabitation of insulators and silencing elements in yeast subtelomeric regions. EMBO J. 18, 2522–2537 (1999).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  30. Teixeira, M. T. et al. Two functionally distinct domains generated by in vivo cleavage of Nup145p: a novel biogenesis pathway for nucleoporins. EMBO J. 16, 5086–5097 (1997).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  31. Sikorski, R. S. & Hieter, P. A system of shuttle vectors and yeast host strains designed for efficient manipulation of DNA in Saccharomyces cerevisiae. Genetics 122, 19–27 (1989).

    CAS  PubMed  PubMed Central  Google Scholar 

  32. Longtine, M. S. et al. Additional modules for versatile and economical PCR-based gene deletion and modification in Saccharomyces cerevisiae. Yeast 14, 953–961 (1998).

    Article  CAS  PubMed  Google Scholar 

  33. Michaelis, C., Ciosk, R. & Nasmyth, K. Cohesins: chromosomal proteins that prevent premature separation of sister chromatids. Cell 91, 35–45 (1997).

    Article  CAS  PubMed  Google Scholar 

  34. Aris, J. P. & Blobel, G. Yeast nuclear envelope proteins cross react with an antibody against mammalian pore complex proteins. J. Cell Biol. 108, 2059–2067 (1989).

    Article  CAS  PubMed  Google Scholar 

  35. Trelles-Sticken, E., Loidl, J. & Scherthan, H. Bouquet formation in budding yeast: initiation of recombination is not required for meiotic telomere clustering. J. Cell Sci. 112, 651–658 (1999).

    CAS  PubMed  Google Scholar 

  36. Louis, E. J., Naumova, E. S., Lee, A., Naumov, G. & Haber, J. E. The chromosome end in yeast: its mosaic nature and influence on recombinational dynamics. Genetics 136, 789–802 (1994).

    CAS  PubMed  PubMed Central  Google Scholar 

  37. Scherthan, H., Loidl, J., Schuster, T. & Schweizer, D. Meiotic chromosome condensation and pairing in Saccharomyces cerevisiae studied by chromosome painting. Chromosoma 101, 590–595 (1992).

    Article  CAS  PubMed  Google Scholar 

  38. Olivo-Marin, J. Extraction of spots in biological images using multiscale products. Pattern Recog., in press (2001).

Download references

Acknowledgements

We are indebted to R. Sternglanz and D. Zappulla (Stony Brook University, NY), K. Nasmyth (University of Vienna), E. Fabre (Institut Pasteur, Paris) and G. Fourel (ENS, Lyon, France) for their kind gift of strains and plasmids. We thank V. Geli (CNRS, Marseille, France) for critical reading of the manuscript. F. F. is supported by a fellowship from Association Nationale de la Recherche contre le SIDA and V. G. is supported by a fellowship from the French Ministry of Research. Work was supported in part by a grant from the Action pour la Recherche contre le Cancer (ARC).

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Author notes

  1. Frank Feuerbach and Vincent Galy: These authors contributed equally to this work

Authors and Affiliations

  1. Laboratoire de Biologie Cellulaire du Noyau, CNRS URA1773, Institut Pasteur, 25 rue du Dr. Roux, Paris, cedex 15, 75724, France

    Frank Feuerbach, Vincent Galy & Ulf Nehrbass

  2. Unite de Génétique des Interactions Macromoléculaires, Institut Pasteur, 25 rue du Dr. Roux, Paris, cedex 15, 75724, France

    Micheline Fromont-Racine & Alain Jacquier

  3. Laboratoire d'Analyse d'Images Quantitative, Institut Pasteur, 25 rue du Dr. Roux, Paris, cedex 15, 75724, France

    Jean-Christophe Olivo-Marin

  4. Abteilung fuer Humanbiologie, Universitaet Kaiserslautern, Germany

    Edgar Trelles-Sticken & Harry Scherthan

  5. Laboratoire de Biologie Moléculaire et Cellulaire de l'Ecole Normale Supérieure de Lyon, UMR5665 CNRS-ENS, 46 allée d'Italie, Lyon, 69364, France

    Eric Gilson

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Correspondence to Ulf Nehrbass.

Supplementary information

Supplementary figures

Supplemental figure 1. Deletion of NUP60 has no effect on protein import/export. (PDF 2181 kb)

Supplemental figure 2. Deletion of the C terminal part of Nup145p or NUP60 releases telomeres from their perinuclear localization.

Supplemental figure 3. Effect of MLP1 or MLP2 deletion on telomere clustering and localization.

Supplemental figure 4. Deletion of MLP1 or YKU70 leads to partial release of the Sir3p-GFP protein from the nuclear matrix.

Supplementary Methods (DOC 135 kb)

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Feuerbach, F., Galy, V., Trelles-Sticken, E. et al. Nuclear architecture and spatial positioning help establish transcriptional states of telomeres in yeast. Nat Cell Biol 4, 214–221 (2002). https://doi.org/10.1038/ncb756

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