SAGA interacting factors confine sub-diffusion of transcribed genes to the nuclear envelope (original) (raw)

Nature volume 441, pages 770–773 (2006)Cite this article

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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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T. Fischer and all the members of the Nehrbass group for critical discussions, and A. Taddei and S. Gasser for sharing unpublished results.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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Author notes

  1. Auguste Genovesio
    Present address: Institut Pasteur Korea, 39-1, Hawolgok-dong, Sungbuk-gu, Seoul, 136-791, Korea
  2. Susana Rodriguez-Navarro
    Present address: Centro de Investigación Príncipe Felipe, Avda Saler 16, 46013, Valencia, Spain
  3. Ghislain G. Cabal and Auguste Genovesio: *These authors contributed equally to this work

Authors and Affiliations

  1. Unité de Biologie Cellulaire du Noyau,
    Ghislain G. Cabal, Olivier Gadal & Frank Feuerbach-Fournier
  2. Unité d'Analyse d'Images Quantitative,
    Auguste Genovesio, Christophe Zimmer & Jean-Christophe Olivo-Marin
  3. Département de Biologie Cellulaire et Infection, Institut Pasteur, 25 rue du Dr Roux, 75724 cedex 15, Paris, France
    Henri Buc
  4. Biochemie-Zentrum der Universität Heidelberg (BZH), Heidelberg, Im Neuenheimer Feld 328, D-69120, Germany
    Susana Rodriguez-Navarro & Eduard C. Hurt
  5. Laboratoire de Physique Théorique de la Matière Condensée, 4 place Jussieu, 75252 cedex 05, Paris, France
    Annick Lesne
  6. Institut Pasteur Korea, 39-1, Hawolgok-dong, Sungbuk-gu, 136-791, Seoul, Korea
    Ulf Nehrbass
  7. Institut Pasteur Korea, 39-1, Hawolgok-dong, Sungbuk-gu, Seoul, 136-791, Korea
    Susana Rodriguez-Navarro
  8. Centro de Investigación Príncipe Felipe, Avda Saler 16, 46013, Valencia, Spain
    Auguste Genovesio

Authors

  1. Ghislain G. Cabal
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  2. Auguste Genovesio
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  3. Susana Rodriguez-Navarro
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  4. Christophe Zimmer
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  5. Olivier Gadal
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  6. Annick Lesne
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  7. Henri Buc
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  8. Frank Feuerbach-Fournier
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  9. Jean-Christophe Olivo-Marin
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  10. Eduard C. Hurt
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  11. Ulf Nehrbass
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Correspondence toUlf 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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Editorial Summary

In the right place

It is becoming clear that the position of genes within the nucleus can influence their expression, and two groups this week report examples of this in yeast. Cabal et al. find that activation of GAL genes confines them to the nuclear periphery. And Taddei et al. report that simply moving the HXK1 gene, by blocking or encouraging its association with the nuclear periphery, significantly alters gene expression.