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.

  • Article
  • Published:

High-resolution statistical mapping reveals gene territories in live yeast

Abstract

The nonrandom positioning of genes inside eukaryotic cell nuclei is implicated in central nuclear functions. However, the spatial organization of the genome remains largely uncharted, owing to limited resolution of optical microscopy, paucity of nuclear landmarks and moderate cell sampling. We developed a computational imaging approach that creates high-resolution probabilistic maps of subnuclear domains occupied by individual loci in budding yeast through automated analysis of thousands of living cells. After validation, we applied the technique to genes involved in galactose metabolism and ribosome biogenesis. We found that genomic loci are confined to 'gene territories' much smaller than the nucleus, which can be remodeled during transcriptional activation, and that the nucleolus is an important landmark for gene positioning. The technique can be used to visualize and quantify territory positions relative to each other and to nuclear landmarks, and should advance studies of nuclear architecture and function.

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

Access options

Rent or buy this article

Prices vary by article type

from$1.95

to$39.95

Prices may be subject to local taxes which are calculated during checkout

Figure 1: Construction of locus probability map.
Figure 2: Validation of mapping method for different loci and the SPB.
Figure 3: Probability maps of genes involved in galactose metabolism and ribosome biogenesis.
Figure 4: Visualizing the spatial arrangement of gene territories.

Similar content being viewed by others

References

  1. Misteli, T. Beyond the sequence: cellular organization of genome function. Cell 128, 787–800 (2007).

    Article  CAS  Google Scholar 

  2. Lanctot, C. et al. Dynamic genome architecture in the nuclear space: regulation of gene expression in three dimensions. Nat. Rev. Genet. 8, 104–115 (2007).

    Article  CAS  Google Scholar 

  3. Fraser, P. & Bickmore, W. Nuclear organization of the genome and the potential for gene regulation. Nature 447, 413–417 (2007).

    Article  CAS  Google Scholar 

  4. Jhunjhunwala, S. et al. The 3D structure of the immunoglobulin heavy-chain locus: implications for long-range genomic interactions. Cell 133, 265–279 (2008).

    Article  CAS  Google Scholar 

  5. Rauch, J. et al. Light optical precision measurements of the active and inactive Prader-Willi syndrome imprinted regions in human cell nuclei. Differentiation 76, 66–82 (2008).

    Article  CAS  Google Scholar 

  6. Haber, J.E. & Leung, W.Y. Lack of chromosome territoriality in yeast: promiscuous rejoining of broken chromosome ends. Proc. Natl. Acad. Sci. USA 93, 13949–13954 (1996).

    Article  CAS  Google Scholar 

  7. Lorenz, A. et al. Spatial organisation and behaviour of the parental chromosome sets in the nuclei of Saccharomyces cerevisiae × S. paradoxus hybrids. J. Cell Sci. 115, 3829–3835 (2002).

    Article  CAS  Google Scholar 

  8. Robinett, C.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 

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

    Article  Google Scholar 

  10. Dieppois, G., Iglesias, N. & Stutz, F. Cotranscriptional recruitment to the mRNA export receptor Mex67p contributes to nuclear pore anchoring of activated genes. Mol. Cell. Biol. 26, 7858–7870 (2006).

    Article  CAS  Google Scholar 

  11. Cabal, G.G. et al. SAGA interacting factors confine sub-diffusion of transcribed genes to the nuclear envelope. Nature 441, 770–773 (2006).

    Article  CAS  Google Scholar 

  12. 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 

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

    Article  CAS  Google Scholar 

  14. Taddei, A. Active genes at the nuclear pore complex. Curr. Opin. Cell Biol. 19, 305–310 (2007).

    Article  CAS  Google Scholar 

  15. Shiels, C. et al. Quantitative analysis of cell nucleus organisation. PLoS Comput. Biol. 3, e138 (2007).

    Article  Google Scholar 

  16. Jin, Q.W., Fuchs, J. & Loidl, J. Centromere clustering is a major determinant of yeast interphase nuclear organization. J. Cell Sci. 113, 1903–1912 (2000).

    CAS  PubMed  Google Scholar 

  17. 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 

  18. Bystricky, K. et al. Chromosome looping in yeast: telomere pairing and coordinated movement reflect anchoring efficiency and territorial organization. J. Cell Biol. 168, 375–387 (2005).

    Article  CAS  Google Scholar 

  19. Thompson, M., Haeusler, R.A., Good, P.D. & Engelke, D.R. Nucleolar clustering of dispersed tRNA genes. Science 302, 1399–1401 (2003).

    Article  CAS  Google Scholar 

  20. Jorgensen, P. et al. A dynamic transcriptional network communicates growth potential to ribosome synthesis and critical cell size. Genes Dev. 18, 2491–2505 (2004).

    Article  CAS  Google Scholar 

  21. Shaner, N.C. et al. Improved monomeric red, orange and yellow fluorescent proteins derived from Discosoma sp. red fluorescent protein. Nat. Biotechnol. 22, 1567–1572 (2004).

    Article  CAS  Google Scholar 

  22. Yang, C.H. et al. Higher order structure is present in the yeast nucleus: autoantibody probes demonstrate that the nucleolus lies opposite the spindle pole body. Chromosoma 98, 123–128 (1989).

    Article  CAS  Google Scholar 

  23. Léger-Silvestre, I., Trumtel, S., Noaillac-Depeyre, J. & Gas, N. Functional compartmentalization of the nucleus in the budding yeast Saccharomyces cerevisiae. Chromosoma 108, 103–113 (1999).

    Article  Google Scholar 

  24. Dorn, J.F. et al. Yeast kinetochore microtubule dynamics analyzed by high-resolution three-dimensional microscopy. Biophys. J. 89, 2835–2854 (2005).

    Article  CAS  Google Scholar 

  25. Heun, P. et al. Chromosome dynamics in the yeast interphase nucleus. Science 294, 2181–2186 (2001).

    Article  CAS  Google Scholar 

  26. Osborne, C.S. et al. Active genes dynamically colocalize to shared sites of ongoing transcription. Nat. Genet. 36, 1065–1071 (2004).

    Article  CAS  Google Scholar 

  27. Berger, A.B. et al. Hmo1 is required for TOR-dependent regulation of ribosomal protein gene transcription. Mol. Cell. Biol. 27, 8015–8026 (2007).

    Article  CAS  Google Scholar 

  28. Marshall, W.F. et al. Interphase chromosomes undergo constrained diffusional motion in living cells. Curr. Biol. 7, 930–939 (1997).

    Article  CAS  Google Scholar 

  29. Therizols, P. et al. Telomere tethering at the nuclear periphery is essential for efficient DNA double strand break repair in subtelomeric region. J. Cell Biol. 172, 189–199 (2006).

    Article  CAS  Google Scholar 

  30. Léger-Silvestre, I., Noaillac-Depeyre, J., Faubladier, M. & Gas, N. Structural and functional analysis of the nucleolus of the fission yeast Schizosaccharomyces pombe. Eur. J. Cell Biol. 72, 13–23 (1997).

    PubMed  Google Scholar 

  31. Ralph, S.A., Scheidig-Benatar, C. & Scherf, A. Antigenic variation in Plasmodium falciparum is associated with movement of var loci between subnuclear locations. Proc. Natl. Acad. Sci. USA 102, 5414–5419 (2005).

    Article  CAS  Google Scholar 

Download references

Acknowledgements

We thank M. Lelek, G. Hubert and A. Couesnon for performing imaging experiments and C. Machu, P. Roux and S. Shorte of the Plateforme d'Imagerie Dynamique (Institut Pasteur) for assistance with microscopy; R. Tilte for programming the nucleus-detection module; R. Tsien (University of California, San Diego) and F. Feuerbach (Institut Pasteur) for providing plasmids; and F. Feuerbach, K. Bystricky, P. Thérizols, B. Zhang, D. Baddeley, A. Lesne, A. Rosa, M. Mhlanga, S. Bachellier, S. Bottani, O. Bischof and X. Darzacq for helpful suggestions or critical reading of an earlier version of the manuscript. A.B.B. was supported by fellowships from the French Ministry of Research and Technology and the German Academic Exchange Service. G.G.C. was recipient of a fellowship from the Association pour la Recherche sur le Cancer. E.F. benefited from Association pour la Recherche sur le Cancer grant 3266. T.D. was funded by Institut Pasteur. O.G. was funded by grants from Centre National de la Recherche Scientifique, Fondation pour la Recherche Médicale and Agence Nationale pour la Recherche. This work was funded by Institut Pasteur through 'Programme Transversal de Recherches' grants to O.G. and C.Z.

Author information

Authors and Affiliations

Authors

Contributions

O.G. and C.Z. designed the method; C.Z. designed computational tools; A.B.B. and O.G. validated computational tools; A.B.B., G.G.C., O.G. and C.Z. designed experiments; A.B.B., G.G.C. and O.G. performed experiments; A.B.B., G.G.C., E.F. and O.G. constructed genetic tools and strains; A.B.B., G.G.C., E.F., H.B., O.G. and C.Z. analyzed and interpreted data; T.D. designed statistical tests; U.N. and J.-C.O.-M. provided initial motivation and scientific environment for research; C.Z. wrote the paper; and A.B.B., G.G.C., E.F., H.B. and O.G. edited the paper.

Corresponding authors

Correspondence to Olivier Gadal or Christophe Zimmer.

Supplementary information

Supplementary Text and Figures

Supplementary Figures 1–5, Supplementary Notes 1–7 (PDF 4319 kb)

Rights and permissions

Reprints and permissions

About this article

Cite this article

Berger, A., Cabal, G., Fabre, E. et al. High-resolution statistical mapping reveals gene territories in live yeast. Nat Methods 5, 1031–1037 (2008). https://doi.org/10.1038/nmeth.1266

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/nmeth.1266

This article is cited by

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