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High-resolution statistical mapping reveals gene territories in live yeast

Nature Methods volume 5, pages 1031–1037 (2008)Cite this article

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.

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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.

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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.

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Author notes

  1. Ghislain G Cabal & Ulf Nehrbass

    Present address: Present addresses: Instituto de Medicina Molecular, Unidade de Malaria, Av. Professor Egas Moniz, 1649-028 Lisboa, Portugal (G.G.C.) and Institut Pasteur Korea, 39-1, Hawolgok-dong, Sungbuk-gu, Seoul 136-791, Korea (U.N.).,

Authors and Affiliations

  1. Institut Pasteur, Unité de Biologie Cellulaire du Noyau, Centre National de la Recherche Scientifique, Unité de Recherche Associée 2582, 25-28 rue du Docteur Roux, Paris, 75015, France

    Axel B Berger, Ghislain G Cabal, Ulf Nehrbass & Olivier Gadal

  2. Institut Pasteur, Unité de Génétique Moléculaire des Levures, Centre National de la Recherche Scientifique, Unité de Recherche Associée 2171, 25-28 rue du Docteur Roux, Paris, 75015, France

    Emmanuelle Fabre

  3. Institut Pasteur, Groupe Imagerie et Modélisation, Centre National de la Recherche Scientifique, Unité de Recherche Associée 2582, 25-28 rue du Docteur Roux, Paris, 75015, France

    Tarn Duong & Christophe Zimmer

  4. Département de Biologie Cellulaire et Infections, Institut Pasteur, Centre National de la Recherche Scientifique, Unité de Recherche Associée 2582, 25-28 rue du Docteur Roux, Paris, 75015, France

    Henri Buc

  5. Institut Pasteur, Unité d'Analyse d'Images Quantitative, Centre National de la Recherche Scientifique, Unité de Recherche Associée 2582, 25-28 rue du Docteur Roux, Paris, 75015, France

    Jean-Christophe Olivo-Marin

  6. Laboratoire de Biologie Moléculaire des Eucaryotes, Centre National de la Recherche Scientifique, Unité Mixte de Recherche 5099, Université de Toulouse, 118 route de Narbonne, Toulouse, 31000, France

    Olivier Gadal

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  1. Axel B Berger
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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.

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

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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

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