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

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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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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