C. elegans ORFeome version 1.1: experimental verification of the genome annotation and resource for proteome-scale protein expression (original) (raw)

• Article
• Published: 07 April 2003
• Philippe Vaglio1 na1,
• Jean-François Rual1,2 na1,
• Philippe Lamesch1,2 na1,
• Monica Martinez1,
• Christopher M. Armstrong1,
• Siming Li1,
• Laurent Jacotot1,
• Nicolas Bertin1,
• Rekin's Janky1,
• Troy Moore3 nAff12,
• James R. Hudson Jr.3 nAff13,
• James L. Hartley4 nAff14,
• Michael A. Brasch4 nAff15,
• Jean Vandenhaute2,
• Simon Boulton1 nAff16,
• Gregory A. Endress5,
• Sarah Jenna6,
• Eric Chevet6,
• Vasilis Papasotiropoulos7,
• Peter P. Tolias7,
• Jason Ptacek8,
• Mike Snyder8,
• Raymond Huang9,
• Mark R. Chance9,
• Hongmei Lee10,
• Lynn Doucette-Stamm10 nAff17,
• David E. Hill1 &
• …
• Marc Vidal1

Nature Genetics volume 34, pages 35–41 (2003)Cite this article

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Abstract

To verify the genome annotation and to create a resource to functionally characterize the proteome, we attempted to Gateway-clone all predicted protein-encoding open reading frames (ORFs), or the 'ORFeome,' of Caenorhabditis elegans. We successfully cloned approximately 12,000 ORFs (ORFeome 1.1), of which roughly 4,000 correspond to genes that are untouched by any cDNA or expressed-sequence tag (EST). More than 50% of predicted genes needed corrections in their intron-exon structures. Notably, approximately 11,000 C. elegans proteins can now be expressed under many conditions and characterized using various high-throughput strategies, including large-scale interactome mapping. We suggest that similar ORFeome projects will be valuable for other organisms, including humans.

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Acknowledgements

We thank the C. elegans Sequencing Consortium for the genome sequence; the participants of the annual ORFeome meeting for their input and numerous suggestions; the members of M.V.'s laboratory for their input and help; C. McCowan for administrative assistance; B. Sobhian, A.-S. Nicot, N. Tzellas and the GenomeVision Service sequencing staff at Genome Therapeutics for technical assistance; and P. Braun for the protein expression plasmids. This work was supported by grants from the National Cancer Institute, the National Human Genome Research Institute, the National Institute of General Medical Sciences and the Merck Genome Research Institute awarded to M.V.

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Author notes

1. Jérôme Reboul
   Present address: INSERM Unité 119, Institut Paoli Calmette, 13009, Marseille, France
2. Troy Moore
   Present address: Open Biosystems, Huntsville, Alabama, 35806, USA
3. James R. Hudson Jr.
   Present address: Cityscapes, Huntsville, Alabama, 35801, USA
4. James L. Hartley
   Present address: SAIC/National Cancer Institute, Frederick, Maryland, 21702, USA
5. Michael A. Brasch
   Present address: Atto Bioscience, Rockville, Maryland, 20850, USA
6. Simon Boulton
   Present address: Cancer Research UK, Clare Hall, Herts, EN6 3LD, UK
7. Lynn Doucette-Stamm
   Present address: Agencourt Biosciences Corporation, Beverly, Massachusetts, 01915, USA
8. Jérôme Reboul, Philippe Vaglio, Jean-François Rual and Philippe Lamesch: These authors contributed equally to this work.

Authors and Affiliations

1. Dana-Farber Cancer Institute and Department of Genetics, Harvard Medical School, Boston, 02115, Massachusetts, USA
   Jérôme Reboul, Philippe Vaglio, Jean-François Rual, Philippe Lamesch, Monica Martinez, Christopher M. Armstrong, Siming Li, Laurent Jacotot, Nicolas Bertin, Rekin's Janky, Simon Boulton, David E. Hill & Marc Vidal
2. Unité de Recherche en Biologie Moléculaire, Facultés Universitaires Notre-Dame de la Paix, Namur, 5000, Belgium
   Jean-François Rual, Philippe Lamesch & Jean Vandenhaute
3. Research Genetics /Invitrogen, Huntsville, Alabama, USA
   Troy Moore & James R. Hudson Jr.
4. Life Technologies /Invitrogen, Rockville, Maryland, USA
   James L. Hartley & Michael A. Brasch
5. Protedyne Corporation, Windsor, 06095, Connecticut, USA
   Gregory A. Endress
6. Department of Surgery, McGill University, Montreal, Canada
   Sarah Jenna & Eric Chevet
7. Center for Applied Genomics, Public Health Research Institute, Newark, 07103, New Jersey, USA
   Vasilis Papasotiropoulos & Peter P. Tolias
8. Yale University, New Haven, 06520, Connecticut, USA
   Jason Ptacek & Mike Snyder
9. Center for Synchrotron Biosciences and Department of Physiology & Biophysics, Albert Einstein College of Medicine, Bronx, 10461, New York, USA
   Raymond Huang & Mark R. Chance
10. Genome Therapeutics, Waltham, 02453, Massachusetts, USA
    Hongmei Lee & Lynn Doucette-Stamm

Authors

1. Jérôme Reboul
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2. Philippe Vaglio
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3. Jean-François Rual
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4. Philippe Lamesch
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5. Monica Martinez
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6. Christopher M. Armstrong
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7. Siming Li
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8. Laurent Jacotot
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9. Nicolas Bertin
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10. Rekin's Janky
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11. Troy Moore
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12. James R. Hudson Jr.
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13. James L. Hartley
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14. Michael A. Brasch
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15. Jean Vandenhaute
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16. Simon Boulton
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17. Gregory A. Endress
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18. Sarah Jenna
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19. Eric Chevet
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20. Vasilis Papasotiropoulos
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21. Peter P. Tolias
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22. Jason Ptacek
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23. Mike Snyder
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24. Raymond Huang
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25. Mark R. Chance
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26. Hongmei Lee
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27. Lynn Doucette-Stamm
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28. David E. Hill
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29. Marc Vidal
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Corresponding author

Correspondence toMarc Vidal.

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Competing interests

T.M. has financial interests in Open Biosystems, one of the companies responsible for the distribution of the C. elegans ORFeome version 1.1.

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Reboul, J., Vaglio, P., Rual, JF. et al. C. elegans ORFeome version 1.1: experimental verification of the genome annotation and resource for proteome-scale protein expression.Nat Genet 34, 35–41 (2003). https://doi.org/10.1038/ng1140

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• Received: 03 January 2003
• Accepted: 14 March 2003
• Published: 07 April 2003
• Issue Date: May 2003
• DOI: https://doi.org/10.1038/ng1140

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