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SAGA interacting factors confine sub-diffusion of transcribed genes to the nuclear envelope

Abstract

Changes in the transcriptional state of genes have been correlated with their repositioning within the nuclear space1. Tethering reporter genes to the nuclear envelope alone can impose repression2 and recent reports have shown that, after activation, certain genes can also be found closer to the nuclear periphery3,4,5,6. The molecular mechanisms underlying these phenomena have remained elusive. Here, with the use of dynamic three-dimensional tracking of a single locus in live yeast (Saccharomyces cerevisiae) cells, we show that the activation of GAL genes (GAL7, GAL10 and GAL1) leads to a confinement in dynamic motility. We demonstrate that the GAL locus is subject to sub-diffusive movement, which after activation can become constrained to a two-dimensional sliding motion along the nuclear envelope. RNA-fluorescence in situ hybridization analysis after activation reveals a higher transcriptional activity for the peripherally constrained GAL genes than for loci remaining intranuclear. This confinement was mediated by Sus1 and Ada2, members of the SAGA histone acetyltransferase complex, and Sac3, a messenger RNA export factor, physically linking the activated GAL genes to the nuclear-pore-complex component Nup1. Deleting ADA2 or NUP1 abrogates perinuclear GAL confinement without affecting GAL1 transcription. Accordingly, transcriptional activation is necessary but not sufficient for the confinement of GAL genes at the nuclear periphery. The observed real-time dynamic mooring of active GAL genes to the inner side of the nuclear pore complex is in accordance with the ‘gene gating’ hypothesis7.

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Figure 1: In vivo dynamic analysis of movements of GAL genes in three dimensions.
Figure 2: Localization and expression of GAL genes on repression or activation.
Figure 3: Mean-squared-displacement analysis of movements of GAL genes.
Figure 4: Localization of GAL genes in SAGA and NPC mutants.

References

  1. Spector, D. L. The dynamics of chromosome organization and gene regulation. Annu. Rev. Biochem. 72, 573–608 (2003)

    CAS  Article  Google Scholar 

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

    ADS  CAS  Article  Google Scholar 

  3. Casolari, J. M., Brown, C. R., Drubin, D. A., Rando, O. J. & Silver, P. A. Developmentally induced changes in transcriptional program alter spatial organization across chromosomes. Genes Dev. 19, 1188–1198 (2005)

    CAS  Article  Google Scholar 

  4. Casolari, J. M. et al. Genome-wide localization of the nuclear transport machinery couples transcriptional status and nuclear organization. Cell 117, 427–439 (2004)

    CAS  Article  Google Scholar 

  5. Brickner, J. H. & Walter, P. Gene recruitment of the activated INO1 locus to the nuclear membrane. PLoS Biol. 2, e342 (2004)

    Article  Google Scholar 

  6. Menon, B. B. et al. Reverse recruitment: the Nup84 nuclear pore subcomplex mediates Rap1/Gcr1/Gcr2 transcriptional activation. Proc. Natl Acad. Sci. USA 102, 5749–5754 (2005)

    ADS  CAS  Article  Google Scholar 

  7. Blobel, G. Gene gating: a hypothesis. Proc. Natl Acad. Sci. USA 82, 8527–8529 (1985)

    ADS  CAS  Article  Google Scholar 

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

    CAS  Article  Google Scholar 

  9. 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)

    CAS  Article  Google Scholar 

  10. Kimura, H., Sugaya, K. & Cook, P. R. The transcription cycle of RNA polymerase II in living cells. J. Cell Biol. 159, 777–782 (2002)

    CAS  Article  Google Scholar 

  11. Vazquez, J., Belmont, A. S. & Sedat, J. W. Multiple regimes of constrained chromosome motion are regulated in the interphase Drosophila nucleus. Curr. Biol. 11, 1227–1239 (2001)

    CAS  Article  Google Scholar 

  12. Havlin, S. & Ben-Avraham, D. Diffusion in disordered media. Adv. Phys. 51, 187–292 (2002)

    ADS  CAS  Article  Google Scholar 

  13. Bouchaud, J. P. & Georges, A. Anomalous diffusion in disordered media: statistical mechanics, models and physical applications. Phys. Rep. 195, 127–293 (1990)

    ADS  MathSciNet  Article  Google Scholar 

  14. Huisinga, K. L. & Pugh, B. F. A genome-wide housekeeping role for TFIID and a highly regulated stress-related role for SAGA in Saccharomyces cerevisiae. Mol. Cell 13, 573–585 (2004)

    CAS  Article  Google Scholar 

  15. Bhaumik, S. R. & Green, M. R. SAGA is an essential in vivo target of the yeast acidic activator Gal4p. Genes Dev. 15, 1935–1945 (2001)

    CAS  Article  Google Scholar 

  16. Larschan, E. & Winston, F. The S. cerevisiae SAGA complex functions in vivo as a coactivator for transcriptional activation by Gal4. Genes Dev. 15, 1946–1956 (2001)

    CAS  Article  Google Scholar 

  17. Fischer, T. et al. Yeast centrin Cdc31 is linked to the nuclear mRNA export machinery. Nature Cell Biol. 6, 840–848 (2004)

    CAS  Article  Google Scholar 

  18. Fischer, T. et al. The mRNA export machinery requires the novel Sac3p–Thp1p complex to dock at the nucleoplasmic entrance of the nuclear pores. EMBO J. 21, 5843–5852 (2002)

    CAS  Article  Google Scholar 

  19. Rodriguez-Navarro, S. et al. Sus1, a functional component of the SAGA histone acetylase complex and the nuclear pore-associated mRNA export machinery. Cell 116, 75–86 (2004)

    CAS  Article  Google Scholar 

  20. Galy, V. et al. Nuclear retention of unspliced mRNAs in yeast is mediated by perinuclear Mlp1. Cell 116, 63–73 (2004)

    CAS  Article  Google Scholar 

Download references

Acknowledgements

We thank D. Fagegaltier, E. Fabre, P. Therizol, B. Zhang, T. Fischer and all the members of the Nehrbass group for critical discussions, and A. Taddei and S. Gasser for sharing unpublished results. We thank the ‘Plateforme d'imagerie dynamique’ of the Pasteur Institute for providing access to the microscopy facilities. This work was supported by an ACI-BCMS grant. G.G.C. and A.G. were recipients of fellowships of the Ministère Français délégué à la Recherche et aux Nouvelles Technologies. Author Contributions E.C.H. and U.N. conceived the project. G.G.C. did the experiments. S.R.-N. did the RT–PCR experiment. G.G.C. and O.G. conceived the image analysis protocols. A.G. and J.-C.O.-M. conceived the image analysis algorithms in collaboration with G.G.C. and O.G. A.G. implemented the image analysis algorithms. G.G.C. did the image processing and analysis. G.G.C. and C.Z. computed the MSD. G.G.C., O.G., C.Z., H.B. and A.L. interpreted the image analysis results. G.G.C., S.R.-N. and F.F.-F. provided the yeast strains and plasmid constructs. U.N. wrote the paper. F.F.-F. supervised G.G.C. J.-C.O.-M. supervised A.G. J.-C.O.-M., E.C.H. and U.N. are head of the laboratories participating in this work.

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Correspondence to Ulf Nehrbass.

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Supplementary information

Supplementary Movie 1

This movie shows an example of 3D live imaging of GAL genes under repressing condition. Time-lapse confocal microscopy in 3D was performed to track the GAL genes in haploid cells grown in glucose containing medium (see legend in Supplementary Notes). (MOV 1602 kb)

Supplementary Movie 2

This movie shows an example of 3D live imaging of GAL genes under activating condition. Time-lapse confocal microscopy in 3D was performed to track the GAL genes in haploid cells grown in galactose containing medium (see legend in Supplementary Notes). (MOV 1424 kb)

Supplementary Notes

This file contains Supplementary Methods, Supplementary Table 1 and 2, and Supplementary Movie Legends. (PDF 1911 kb)

Supplementary Figures

This file contains Supplementary Figures 1–7 with their legends. (PDF 3661 kb)

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Cabal, G., Genovesio, A., Rodriguez-Navarro, S. et al. SAGA interacting factors confine sub-diffusion of transcribed genes to the nuclear envelope. Nature 441, 770–773 (2006). https://doi.org/10.1038/nature04752

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