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A Y2H-seq approach defines the human protein methyltransferase interactome

Nature Methods volume 10, pages 339–342 (2013)Cite this article

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Abstract

To accelerate high-density interactome mapping, we developed a yeast two-hybrid interaction screening approach involving short-read second-generation sequencing (Y2H-seq) with improved sensitivity and a quantitative scoring readout allowing rapid interaction validation. We applied Y2H-seq to investigate enzymes involved in protein methylation, a largely unexplored post-translational modification. The reported network of 523 interactions involving 22 methyltransferases or demethylases is comprehensively annotated and validated through coimmunoprecipitation experiments and defines previously undiscovered cellular roles of nonhistone protein methylation.

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Figure 1: The Y2H-seq approach.
Figure 2: The protein methyltransferase interactome.
Figure 3: Validation of the Y2H-seq data.

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Acknowledgements

We thank B. Lukaszewska-McGreal from the MPIMG–mass spectrometry group and D. Roth and S. Paturej from the MPIMG–next-generation sequencing team for their experimental support. The work was supported by the Max Planck Society and the German Ministry of Science (NGFNp, NeuroNet-TP3 01GS08171; BMBF, 0315082).

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Author notes

  1. Mareike Weimann, Arndt Grossmann and Jonathan Woodsmith: These authors contributed equally to this work.

Authors and Affiliations

  1. Otto-Warburg Laboratory, Max Planck Institute for Molecular Genetics (MPIMG), Berlin, Germany

    Mareike Weimann, Arndt Grossmann, Jonathan Woodsmith, Ziya Özkan, Petra Birth, David Meierhofer, Nouhad Benlasfer, Bernd Timmermann, Sascha Sauer & Ulrich Stelzl

  2. Institute of Biochemistry, Center for Molecular Biosciences, University of Innsbruck, Innsbruck, Austria

    Taras Valovka

  3. Neuroproteomics Program, Max Delbrück Center for Molecular Medicine, Berlin-Buch, Germany

    Erich E Wanker

Authors
  1. Mareike Weimann
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  4. Ziya Özkan
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Contributions

M.W. performed Y2H screens. A.G. and U.S. developed the screening protocol. J.W. and A.G. analyzed the sequencing data. Z.Ö. contributed to cloning, Y2H and protein purification experiments. P.B. performed the co-IP experiments. M.W. and N.B. performed the methylation assays. D.M. performed the mass spectrometry analysis. T.V., B.T., E.E.W. and S.S. contributed tools and reagents. M.W., J.W. and U.S. analyzed the data and generated the figures. U.S. conceived and supervised the study and wrote the manuscript. All authors provided feedback on the manuscript.

Corresponding author

Correspondence to Ulrich Stelzl.

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The authors declare no competing financial interests.

Supplementary information

Supplementary Text and Figures

Supplementary Figures 1–6 and Supplementary Tables 1,2,4,6 and 7 (PDF 1171 kb)

Supplementary Tables 3 and 5

PPI data. Columns are as follows: Symbol_p NCBI ENTREZ GeneID of the prey protein; GeneID_p, NCBI Entrez symbol of the prey protein;Symbol_b, NCBI Entrez Gene ID of the bait protein (PMTs and PDeMs);GeneID_b, NCBI Entrez Gene ID of the bait protein (PMTs and PDeMs); Y2HRetest, retest result (sum of the fraction of bait-prey combinations found over tested); Matrix, interaction found in the matrix approach; Y2H-seq, interaction found in the Y2H-seq approach. (XLS 100 kb)

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Weimann, M., Grossmann, A., Woodsmith, J. et al. A Y2H-seq approach defines the human protein methyltransferase interactome. Nat Methods 10, 339–342 (2013). https://doi.org/10.1038/nmeth.2397

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