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A radiation hybrid transcript map of the mouse genome

Nature Genetics volume 29, pages 194–200 (2001)Cite this article

An Erratum to this article was published on 01 November 2001

Abstract

Expressed-sequence tag (EST) maps are an adjunct to sequence-based analytical methods of gene detection and localization for those species for which such data are available, and provide anchors for high-density homology and orthology mapping in species for which large-scale sequencing has yet to be done1. Species for which radiation hybrid–based transcript maps have been established include human2, rat3,4,5, mouse6, dog7, cat8 and zebrafish9,10. We have established a comprehensive first-generation–placement radiation hybrid map of the mouse consisting of 5,904 mapped markers (3,993 ESTs and 1,911 sequence-tagged sites (STSs)). The mapped ESTs, which often originate from small-EST clusters, are enriched for genes expressed during early mouse embryogenesis and are probably different from those localized in humans. We have confirmed by in situ hybridization that even singleton ESTs, which are usually not retained for mapping studies, may represent bona fide transcribed sequences. Our studies on mouse chromosomes 12 and 14 orthologous to human chromosome 14 show the power of our radiation hybrid map as a predictive tool for orthology mapping in humans.

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Figure 1: Whole-mount in situ hybridization: singletons represent bona fide gene transcripts.
Figure 2: Placement maps for chromosome 5.
Figure 3: Comprehensive radiation hybrid map of mouse chromosome 2.
Figure 4: Orthologous relationships between mouse ESTs mapping to mouse chromosome 12 and human chromosome 14, showing positions on the radiation hybrid map of mouse chromosome 12 (left-hand bar) and human chromosome 14 (right-hand bars).

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Acknowledgements

We dedicate this article to our friend and colleague Rosa Beddington (March 23, 1956–May 18, 2001), a scientist of great biological insight. This work was supported by EEC Contract PL 962414. We thank B. Gorick and the Human Genome Mapping Project at Hinxton, UK, for help with the replication of the 7.5-dpc mouse endoderm library; A.M. Mallon and S. Greenaway of the informatics group at the Medical Research Council, Harwell; and V. Taghavi and E. Sartory for technical assistance in marker typing at MRC Harwell.

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Author notes

  1. Michael V. Wiles

    Present address: Deltagen Inc., Menlo Park, California, USA

  2. Patricia Rodriguez-Tome

    Present address: Geneva Proteomics Inc., Meyringe, Switzerland

  3. Rosa Beddington: Deceased.

Authors and Affiliations

  1. Genoscope, Centre National de Sequençage and CNRS UMR 8030, CP 5706, Evry Cedex, 91057, France

    Philip Avner, Thomas Bruls, Isabelle Poras, Shahinaz Gas & Jean Weissenbach

  2. Unité de Génétique Moléculaire Murine, Institut Pasteur, Paris, France

    Philip Avner

  3. Mammalian Genetics Unit, Medical Research Council, Harwell, UK

    Lorraine Eley, Liz Bentley, Michelle Goldsworthy, Alison Haynes, Eifion Herbert, Lorraine Southam & Roger D. Cox

  4. Centre de Recherche du CHUL, Ste-Foy, Quebec, Canada

    Patricia Ruiz & Jean Morissette

  5. Max-Planck Institute of Molecular Genetics, Ihnestrasse, Berlin, Germany

    Michael V. Wiles & Hans Lehrach

  6. Laboratory of Mammalian Development, National Institute for Medical Research, The Ridgeway, Mill Hill, London, UK

    Rita Sousa-Nunes, Ross Kettleborough, Amer Rana & Sally Dunwoodie

  7. Division of Oncology, Instituto Nazionale Tumori, Milano, Italy

    Giacomo Manenti

  8. The European Bioinformatics Institute, European Molecular Biology Laboratory Outstation, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK

    Patricia Rodriguez-Tome

  9. The Victor Chang Cardiac Research Institute, Darlinghurst, Sydney, Australia

    Sally Dunwoodie

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Correspondence to Philip Avner.

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Avner, P., Bruls, T., Poras, I. et al. A radiation hybrid transcript map of the mouse genome. Nat Genet 29, 194–200 (2001). https://doi.org/10.1038/ng1001-194

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