Article abstract
Nature Methods 5, 1031 - 1037 (2008)
Published online: 2 November 2008 | doi:10.1038/nmeth.1266
High-resolution statistical mapping reveals gene territories in live yeast
Axel B Berger1, Ghislain G Cabal1,7, Emmanuelle Fabre2, Tarn Duong3, Henri Buc4, Ulf Nehrbass1,7, Jean-Christophe Olivo-Marin5, Olivier Gadal1,6 & Christophe Zimmer3
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.
- 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, 75015 Paris, France.
- 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, 75015 Paris, France.
- Institut Pasteur, Groupe Imagerie et Modélisation, Centre National de la Recherche Scientifique, Unité de Recherche Associée 2582, 25-28 rue du Docteur Roux, 75015 Paris, France.
- Institut Pasteur, Département de Biologie Cellulaire et Infections, Centre National de la Recherche Scientifique, Unité de Recherche Associée 2582, 25-28 rue du Docteur Roux, 75015 Paris, France.
- 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, 75015 Paris, France.
- Laboratoire de Biologie Moléculaire des Eucaryotes, Centre National de la Recherche Scientifique, Unité Mixte de Recherche 5099, Université de Toulouse, 118 route de Narbonne, 31000 Toulouse, France.
- 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.).
Correspondence to: Christophe Zimmer3 e-mail: czimmer@pasteur.fr
Correspondence to: Olivier Gadal1,6 e-mail: olivier.gadal@ibcg.biotoul.fr
