Brief Communication | Published:

A public genome-scale lentiviral expression library of human ORFs

Nature Methods 8, 659–661 (2011) | Download Citation

Subjects

Abstract

Functional characterization of the human genome requires tools for systematically modulating gene expression in both loss-of-function and gain-of-function experiments. We describe the production of a sequence-confirmed, clonal collection of over 16,100 human open-reading frames (ORFs) encoded in a versatile Gateway vector system. Using this ORFeome resource, we created a genome-scale expression collection in a lentiviral vector, thereby enabling both targeted experiments and high-throughput screens in diverse cell types.

Access optionsAccess options

Rent or Buy article

Get time limited or full article access on ReadCube.

from$8.99

Rent or Buy

All prices are NET prices.

References

  1. 1.

    , & Nat. Rev. Genet. 11, 685–696 (2010).

  2. 2.

    1000 Genomes Project Consortium. et al. Nature 467, 1061–1073 (2010).

  3. 3.

    , , & Curr. Opin. Mol. Ther. 12, 284–293 (2010).

  4. 4.

    et al. Genome Res. 14, 2128–2135 (2004).

  5. 5.

    et al. Genomics 89, 307–315 (2007).

  6. 6.

    et al. PLoS ONE 3, e1528 (2008).

  7. 7.

    et al. BMC Genomics 8, 399 (2007).

  8. 8.

    et al. Nat. Methods 5, 1011–1017 (2008).

  9. 9.

    MGC Project Team. et al. Genome Res. 19, 2324–2333 (2009).

  10. 10.

    et al. Nature 437, 1173–1178 (2005).

  11. 11.

    , & Genome Res. 10, 1788–1795 (2000).

  12. 12.

    et al. Methods Enzymol. 328, 575–592 (2000).

  13. 13.

    & Bioinformatics 25, 1754–1760 (2009).

  14. 14.

    et al. Nat. Methods 5, 597–600 (2008).

  15. 15.

    et al. Nature 468, 968–972 (2010).

  16. 16.

    & PCR Methods Appl. 1, 124–128 (1991).

  17. 17.

    et al. Cell 124, 1283–1298 (2006).

  18. 18.

    , , , & J. Gen. Virol. 72, 1551–1557 (1991).

  19. 19.

    , , & J. Virol. 73, 2886–2892 (1999).

Download references

Acknowledgements

We thank B. Piqani, I. Budianto, D. Szeto, T. Hirozane-Kishikawa, V. Swearingen, A. MacWilliams, T. Nieland, S. Hoang, J. Bochicchio, S. Young, A. Berlin, C. Russ, M. Garber and members of the Broad Institute Genetic Sequencing Platform who provided technical assistance or advice throughout this project, and J. Zhao, T. Roberts and T. Golub for participation in kinase ORFs subcollection generation. This work was supported by Broad Institute Scientific Planning and Allocation of Resources Committee funding, The Ellison Foundation (D.E.H. and M.V.), Dana-Farber Cancer Institute sponsored research funds to CCSB and Center for Cancer Genome Discovery and US National Institutes of Health R33 CA128625 (W.C.H., D.E.R. and D.E.H.).

Author information

    • Kourosh Salehi-Ashtiani
    •  & Haley Hieronymus

    Present addresses: New York University Abu Dhabi, Abu Dhabi, United Arab Emirates and Center for Genomics and Systems Biology, Department of Biology, New York University, New York, New York, USA (K.S.-A.) and Human Oncology and Pathogenesis Program, Memorial Sloan-Kettering Cancer Center, New York, New York, USA (H.H.).

    • Xiaoping Yang
    • , Jesse S Boehm
    • , Xinping Yang
    • , Kourosh Salehi-Ashtiani
    • , Tong Hao
    • , Yun Shen
    •  & Rakela Lubonja

    These authors contributed equally to this work.

Affiliations

  1. RNA interference (RNAi) Platform, Broad Institute of Harvard and Massachusetts Institute of Technology (MIT), Cambridge, Massachusetts, USA.

    • Xiaoping Yang
    • , Rakela Lubonja
    • , Ozan Alkan
    • , Tashfeen Bhimdi
    • , Thomas M Green
    • , Serena J Silver
    • , Cindy Nguyen
    •  & David E Root

  2. Cancer Program, Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA.

    • Jesse S Boehm
    • , Sapana R Thomas
    • , Cory M Johannessen
    • , Haley Hieronymus
    •  & William C Hahn

  3. Center for Cancer Systems Biology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA.

    • Xinping Yang
    • , Kourosh Salehi-Ashtiani
    • , Tong Hao
    • , Yun Shen
    • , Ryan R Murray
    • , Dawit Balcha
    • , Changyu Fan
    • , Chenwei Lin
    • , Lila Ghamsari
    • , Marc Vidal
    • , William C Hahn
    •  & David E Hill

  4. Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA.

    • Xinping Yang
    • , Kourosh Salehi-Ashtiani
    • , Tong Hao
    • , Yun Shen
    • , Ryan R Murray
    • , Dawit Balcha
    • , Changyu Fan
    • , Chenwei Lin
    • , Lila Ghamsari
    • , Marc Vidal
    •  & David E Hill

  5. Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA.

    • Xinping Yang
    • , Kourosh Salehi-Ashtiani
    • , Tong Hao
    • , Yun Shen
    • , Ryan R Murray
    • , Dawit Balcha
    • , Changyu Fan
    • , Chenwei Lin
    • , Lila Ghamsari
    • , Marc Vidal
    •  & David E Hill

  6. Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA.

    • Cory M Johannessen
    •  & William C Hahn

  7. Center for Cancer Genome Discovery, Dana-Farber Cancer Institute, Boston, Massachusetts, USA.

    • Cory M Johannessen
    •  & William C Hahn

  8. Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, USA.

    • Haley Hieronymus

Authors

  1. Search for Xiaoping Yang in:

  2. Search for Jesse S Boehm in:

  3. Search for Xinping Yang in:

  4. Search for Kourosh Salehi-Ashtiani in:

  5. Search for Tong Hao in:

  6. Search for Yun Shen in:

  7. Search for Rakela Lubonja in:

  8. Search for Sapana R Thomas in:

  9. Search for Ozan Alkan in:

  10. Search for Tashfeen Bhimdi in:

  11. Search for Thomas M Green in:

  12. Search for Cory M Johannessen in:

  13. Search for Serena J Silver in:

  14. Search for Cindy Nguyen in:

  15. Search for Ryan R Murray in:

  16. Search for Haley Hieronymus in:

  17. Search for Dawit Balcha in:

  18. Search for Changyu Fan in:

  19. Search for Chenwei Lin in:

  20. Search for Lila Ghamsari in:

  21. Search for Marc Vidal in:

  22. Search for William C Hahn in:

  23. Search for David E Hill in:

  24. Search for David E Root in:

Contributions

J.S.B., Xia. Y. and D.E.R. wrote the manuscript and, together with D.E.H., K.S.-A. and M.V., designed and supervised the process of creating clonal sequenced ORF collections. Xin. Y., D.B., L.G., J.S.B., S.R.T., H.H., R.R.M., K.S.-A. and C.M.J. generated the starting collections of ORFs. R.L., O.A., J.S.B., C.N., Xia. Y., S.J.S., S.R.T. and C.M.J. created the final libraries, DNA, viruses and pLX vectors, and evaluated expression. T.H., Y.S., C.F., C.L., J.S.B., T.B., T.M.G., Xia. Y. and D.E.R. performed bioinformatic analyses. M.V., W.C.H., D.E.H. and D.E.R. supervised the project.

Competing interests

The authors declare no competing financial interests.

Corresponding authors

Correspondence to Marc Vidal or William C Hahn or David E Hill or David E Root.

Supplementary information

PDF files

  1. 1.

    Supplementary Text and Figures

    Supplementary Figures 1–12, Supplementary Tables 1–4; Supplementary Notes 1–8

To obtain permission to re-use content from this article visit RightsLink.

About this article

Publication history

Received

Accepted

Published

DOI

https://doi.org/10.1038/nmeth.1638