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Yeast one-hybrid assays for gene-centered human gene regulatory network mapping

Nature Methods volume 8, pages 1050–1052 (2011)Cite this article

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Abstract

Gateway-compatible yeast one-hybrid (Y1H) assays provide a convenient gene-centered (DNA to protein) approach to identify transcription factors that can bind a DNA sequence of interest. We present Y1H resources, including clones for 988 of 1,434 (69%) predicted human transcription factors, that can be used to detect both known and new interactions between human DNA regions and transcription factors.

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Figure 1: Human gene-centered Y1H assays.
Figure 2: eY1H data analysis.

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Acknowledgements

We thank members of the Walhout lab for discussions and critical reading of the manuscript. Research in the Walhout lab is supported by US National Institutes of Health (NIH) grants DK068429 and GM082971. This work was supported by NIH grant HG003143 and a W.M. Keck Foundation Distinguished Young scholar award to J.D., an Ellison Foundation grant and Dana Farber Cancer Institute Sponsored Research funds awarded to Center for Cancer Systems Biology. Research in the Blackshaw lab is funded by a W.M. Keck Foundation Distinguished Young scholar award and a grant from the Ruth and Milton Steinbach Fund. H.Z. is supported by NIH grant GM076102.

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Authors and Affiliations

  1. Program in Systems Biology, University of Massachusetts Medical School, Worcester, Massachusetts, USA

    John S Reece-Hoyes, Rachel Patton McCord, Job Dekker & Albertha J M Walhout

  2. Program in Gene Function and Expression, University of Massachusetts Medical School, Worcester, Massachusetts, USA

    John S Reece-Hoyes, A Rasim Barutcu, Rachel Patton McCord, Job Dekker & Albertha J M Walhout

  3. Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, Massachusetts, USA

    John S Reece-Hoyes & Albertha J M Walhout

  4. Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts, USA

    A Rasim Barutcu, Rachel Patton McCord & Job Dekker

  5. Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA

    Jun Seop Jeong, Lizhi Jiang, Seth Blackshaw & Heng Zhu

  6. Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA

    Jun Seop Jeong, Lizhi Jiang, Seth Blackshaw & Heng Zhu

  7. Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA

    Jun Seop Jeong, Lizhi Jiang, Seth Blackshaw & Heng Zhu

  8. Department of Ophthalmology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA

    Jun Seop Jeong, Lizhi Jiang, Seth Blackshaw & Heng Zhu

  9. Center for High-Throughput Biology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA

    Jun Seop Jeong, Lizhi Jiang, Seth Blackshaw & Heng Zhu

  10. Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA

    Jun Seop Jeong, Lizhi Jiang, Seth Blackshaw & Heng Zhu

  11. Center for Cancer Systems Biology and Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA

    Andrew MacWilliams, Xinping Yang, Kourosh Salehi-Ashtiani, David E Hill, Job Dekker & Albertha J M Walhout

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

    Andrew MacWilliams, Xinping Yang, Kourosh Salehi-Ashtiani & David E Hill

Authors
  1. John S Reece-Hoyes
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  2. A Rasim Barutcu
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  3. Rachel Patton McCord
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  4. Jun Seop Jeong
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  5. Lizhi Jiang
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  6. Andrew MacWilliams
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  7. Xinping Yang
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  8. Kourosh Salehi-Ashtiani
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  9. David E Hill
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  10. Seth Blackshaw
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  11. Heng Zhu
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  12. Job Dekker
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  13. Albertha J M Walhout
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Contributions

A.J.M.W. conceived the project; J.D., J.S.R.-H. and A.J.M.W. designed the project; J.S.R.-H. and A.R.B. performed the experiments; J.S.R.-H. and A.J.M.W. analyzed the data; J.S.J., L.J. and A.M. picked transcription factor ORF clones; J.S.J. and L.J. assisted A.R.B. and J.S.R.-H. with Gateway cloning. R.P.M. performed the binding-site analysis; H.Z., S.B., K.S.-A., X.Y., A.M. and D.E.H. provided transcription factor ORFeome clones; J.S.R.-H. and A.J.M.W. wrote the manuscript.

Corresponding authors

Correspondence to John S Reece-Hoyes or Albertha J M Walhout.

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The authors declare no competing financial interests.

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Supplementary Figures 1–3 and Supplementary Tables 1–9 (PDF 4942 kb)

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Reece-Hoyes, J., Barutcu, A., McCord, R. et al. Yeast one-hybrid assays for gene-centered human gene regulatory network mapping. Nat Methods 8, 1050–1052 (2011). https://doi.org/10.1038/nmeth.1764

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