Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

Nuclear pore association confers optimal expression levels for an inducible yeast gene

Abstract

The organization of the nucleus into subcompartments creates microenvironments that are thought to facilitate distinct nuclear functions1. In budding yeast, regions of silent chromatin, such as those at telomeres and mating-type loci, cluster at the nuclear envelope creating zones that favour gene repression1,2. Other reports indicate that gene transcription occurs at the nuclear periphery, apparently owing to association of the gene with nuclear pore complexes3,4,5. Here we report that transcriptional activation of a subtelomeric gene, HXK1 (hexokinase isoenzyme 1), by growth on a non-glucose carbon source led to its relocalization to nuclear pores. This relocation required the 3′ untranslated region (UTR), which is essential for efficient messenger RNA processing and export, consistent with an accompanying report6. However, activation of HXK1 by an alternative pathway based on the transactivator VP16 moved the locus away from the nuclear periphery and abrogated the normal induction of HXK1 by galactose. Notably, when we interfered with HXK1 localization by either antagonizing or promoting association with the pore, transcript levels were reduced or enhanced, respectively. From this we conclude that nuclear position has an active role in determining optimal gene expression levels.

This is a preview of subscription content, access via your institution

Relevant articles

Open Access articles citing this article.

Access options

Buy article

Get time limited or full article access on ReadCube.

$32.00

All prices are NET prices.

Figure 1: Relocation of HXK1 to the nuclear periphery on galactose requires the 3′ UTR.
Figure 2: HXK1 colocalizes with nuclear pores in glucose-free medium.
Figure 3: Alternative modes of transcriptional activation displace Tel6R from the nuclear periphery.
Figure 4: Impairing or improving perinuclear anchoring modulates HXK1 transcript levels on galactose.

References

  1. Taddei, A., Hediger, F., Neumann, F. R. & Gasser, S. M. The function of nuclear architecture: a genetic approach. Annu. Rev. Genet. 38, 305–345 (2004)

    Article  CAS  Google Scholar 

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

    Article  ADS  Google Scholar 

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

    Article  CAS  Google Scholar 

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

    Article  Google Scholar 

  5. 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)

    Article  CAS  Google Scholar 

  6. Cabal, G. G. et al. SAGA interacting factors confine sub-diffusion of transcribed genes to the nuclear envelope. Nature doi:10.1038/nature04752 (this issue)

  7. Hediger, F., Neumann, F. R., Van Houwe, G., Dubrana, K. & Gasser, S. M. Live imaging of telomeres. yKu and Sir proteins define redundant telomere-anchoring pathways in yeast. Curr. Biol. 12, 2076–2089 (2002)

    Article  CAS  Google Scholar 

  8. Taddei, A., Hediger, F., Neumann, F. R., Bauer, C. & Gasser, S. M. Separation of silencing from perinuclear anchoring functions in yeast Ku80, Sir4 and Esc1 proteins. EMBO J. 23, 1301–1312 (2004)

    Article  CAS  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)

    Article  CAS  Google Scholar 

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

    Article  ADS  CAS  Google Scholar 

  11. Robinett, C. et al. In vivo localization of DNA sequences and visualization of large scale chromatin organization using lac-operator/repressor recognition. J. Cell Biol. 135, 1685–1700 (1996)

    Article  CAS  Google Scholar 

  12. Heun, P., Laroche, T., Shimada, K., Furrer, P. & Gasser, S. M. Chromosome dynamics in the yeast interphase nucleus. Science 294, 2181–2186 (2001)

    Article  ADS  CAS  Google Scholar 

  13. de la Cera, T., Herrero, P., Moreno-Herrero, F., Chaves, R. S. & Moreno, F. Mediator factor Med8p interacts with the hexokinase 2: implication in the glucose signalling pathway of Saccharomyces cerevisiae. J. Mol. Biol. 319, 703–714 (2002)

    Article  CAS  Google Scholar 

  14. Rodriguez, A., de la Cera, T., Herrero, P. & Moreno, F. The hexokinase 2 protein regulates the expression of the GLK1, HXK1 and HXK2 genes of Saccharomyces cerevisiae. Biochem. J. 355, 625–631 (2001)

    Article  CAS  Google Scholar 

  15. Sadowski, I., Ma, J., Triezenberg, S. & Ptashne, M. GAL4–VP16 is an unusually potent transcriptional activator. Nature 335, 563–564 (1988)

    Article  ADS  CAS  Google Scholar 

  16. Tham, W. H., Wyithe, J. S., Ko Ferrigno, P., 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  Google Scholar 

  17. Hediger, F., Berthiau, A. S., van Houwe, G., Gilson, E. & Gasser, S. M. Subtelomeric factors antagonize telomere anchoring and Tel1-independent telomere length regulation. EMBO J. 25, 857–867 (2006)

    Article  CAS  Google Scholar 

  18. Ishii, K., Arib, G., Lin, C., Van Houwe, G. & Laemmli, U. K. Chromatin boundaries in budding yeast: the nuclear pore connection. Cell 109, 551–562 (2002)

    Article  CAS  Google Scholar 

  19. 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)

    Article  ADS  CAS  Google Scholar 

  20. Gill, G. & Ptashne, M. Negative effect of the transcriptional activator GAL4. Nature 334, 721–724 (1988)

    Article  ADS  CAS  Google Scholar 

  21. Ito, T. et al. A comprehensive two-hybrid analysis to explore the yeast protein interactome. Proc. Natl Acad. Sci. USA 98, 4569–4574 (2001)

    Article  ADS  CAS  Google Scholar 

  22. Gavin, A. C. et al. Functional organization of the yeast proteome by systematic analysis of protein complexes. Nature 415, 141–147 (2002)

    Article  ADS  CAS  Google Scholar 

  23. O'Sullivan, J. M. et al. Gene loops juxtapose promoters and terminators in yeast. Nature Genet. 36, 1014–1018 (2004)

    Article  CAS  Google Scholar 

  24. Hediger, F., Taddei, A., Neumann, F. R. & Gasser, S. M. Methods for visualizing chromatin dynamics in living yeast. Methods Enzymol. 375, 345–365 (2004)

    Article  CAS  Google Scholar 

  25. Sage, D., Neumann, F. R., Hediger, F., Gasser, S. M. & Unser, M. Automatic tracking of individual fluorescence particles: application to the study of chromosome dynamics. IEEE Trans. Image Process. 14, 1372–1383 (2005)

    Article  ADS  Google Scholar 

  26. Gartenberg, M. R., Neumann, F. R., Laroche, T., Blaszczyk, M. & Gasser, S. M. Sir-mediated repression can occur independently of chromosomal and subnuclear contexts. Cell 119, 955–967 (2004)

    Article  CAS  Google Scholar 

  27. Vandesompele, J. et al. Accurate normalization of real-time quantitative RT-PCR data by geometric averaging of multiple internal control genes. Genome Biol. 3, research0034.1–research0034.11 (2002)

  28. Schmid, M. et al. Nup-PI: The nucleopore-promoter interaction of genes in yeast. Mol Cell 21, 379–391 (2006)

    Article  CAS  Google Scholar 

Download references

Acknowledgements

We thank T. Laroche, the imaging platform of the FMI, and the genomics platform of the NCCR for assistance, and E. Heard, A. Peters, G. Almouzni, D. Schübeler and M. Gartenberg for helpful suggestions, as well as G. Cabal and U. Nehrbass for sharing unpublished results. Our research is supported by the Swiss National Science Foundation, the NCCR programme ‘Frontiers in Genetics’, and the Novartis Research Foundation.

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Susan M. Gasser.

Ethics declarations

Competing interests

Reprints and permissions information is available at npg.nature.com/reprintsandpermissions. The authors declare no competing financial interests.

Supplementary information

Supplementary Notes

This file contains Supplementary Tables 1–3 and Supplementary Figure Legends. (DOC 70 kb)

Supplementary Figure 1

Abundance of the elongation-specific form of the RNA pol II on HXK1. (PDF 17 kb)

Supplementary Figure 2

HXK1 dynamics on glucose versus galactose media. (PDF 42 kb)

Supplementary Figure 3

Targeted VP16 allows variegated expression of subtelomeric ADE2 gene. (PDF 32 kb)

Supplementary Figure 4

VP16 targeting increases HXK1 dynamics. (PDF 35 kb)

Rights and permissions

Reprints and Permissions

About this article

Cite this article

Taddei, A., Van Houwe, G., Hediger, F. et al. Nuclear pore association confers optimal expression levels for an inducible yeast gene. Nature 441, 774–778 (2006). https://doi.org/10.1038/nature04845

Download citation

  • Received:

  • Accepted:

  • Issue Date:

  • DOI: https://doi.org/10.1038/nature04845

This article is cited by

Comments

By submitting a comment you agree to abide by our Terms and Community Guidelines. If you find something abusive or that does not comply with our terms or guidelines please flag it as inappropriate.

Search

Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing