Human ORFeome Version 1.1: A Platform for Reverse Proteomics

  1. Jean-François Rual1,2,9,
  2. Tomoko Hirozane-Kishikawa1,9,
  3. Tong Hao1,9,
  4. Nicolas Bertin1,3,9,
  5. Siming Li1,9,
  6. Amélie Dricot1,
  7. Ning Li1,
  8. Jennifer Rosenberg1,
  9. Philippe Lamesch1,2,
  10. Pierre-Olivier Vidalain1,
  11. Tracey R. Clingingsmith1,
  12. James L. Hartley4,
  13. Dominic Esposito4,
  14. David Cheo6,
  15. Troy Moore6,
  16. Blake Simmons6,
  17. Reynaldo Sequerra7,
  18. Stephanie Bosak7,
  19. Lynn Doucette-Stamm7,
  20. Christian Le Peuch3,
  21. Jean Vandenhaute2,
  22. Michael E. Cusick1,
  23. Joanna S. Albala1,8,
  24. David E. Hill1,10, and
  25. Marc Vidal1,10
  1. 1 Center for Cancer Systems Biology and Department of Cancer Biology, Dana-Farber Cancer Institute and Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
  2. 2 Facultés Universitaires Notre-Dame de la Paix, 5000 Namur, Belgium
  3. 3 Centre de Recherche en Biochimie Macromoleculaire, Centre National de la Recherche Scientifique FRE 2593, 34293 Montpellier Cedex 5, France
  4. 4 Science Applications International Corporation/National Cancer Institute, Frederick, Maryland 21702, USA
  5. 5 Atto Bioscience, Rockville, Maryland 20850, USA
  6. 6 Open Biosystems, Inc., Huntsville, Alabama 35806, USA
  7. 7 Agencourt Biosciences Corporation, Beverly, Massachusetts 01915, USA
  8. 8 Biology and Biotechnology Research Program, Lawrence Livermore National Laboratory, University of California, Livermore, California 94551, USA

Abstract

The advent of systems biology necessitates the cloning of nearly entire sets of protein-encoding open reading frames (ORFs), or ORFeomes, to allow functional studies of the corresponding proteomes. Here, we describe the generation of a first version of the human ORFeome using a newly improved Gateway recombinational cloning approach. Using the Mammalian Gene Collection (MGC) resource as a starting point, we report the successful cloning of 8076 human ORFs, representing at least 7263 human genes, as mini-pools of PCR-amplified products. These were assembled into the human ORFeome version 1.1 (hORFeome v1.1) collection. After assessing the overall quality of this version, we describe the use of hORFeome v1.1 for heterologous protein expression in two different expression systems at proteome scale. The hORFeome v1.1 represents a central resource for the cloning of large sets of human ORFs in various settings for functional proteomics of many types, and will serve as the foundation for subsequent improved versions of the human ORFeome.

Footnotes

  • [Supplemental material is available online at www.genome.org.]

  • Article and publication are at http://www.genome.org/cgi/doi/10.1101/gr.2973604.

  • ↵9 These authors contributed equally to this work.

  • ↵10 Corresponding authors. E-MAIL marc_vidal{at}dfci.harvard.edu; FAX (617) 632-5739. E-MAIL david_hill{at}dfci.harvard.edu; FAX (617) 632-5739.

    • Accepted August 19, 2004.
    • Received July 7, 2004.
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  1. doi: 10.1101/gr.2973604 Genome Res. 14: 2128-2135 Cold Spring Harbor Laboratory Press

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