Mapping transcription factor interactome networks using HaloTag protein arrays

Junshi Yazaki, Mary Galli, Alice Y. Kim, Kazumasa Nito, Fernando Aleman, Katherine N. Chang, Anne Ruxandra Carvunis, Rosa Quan, Hien Nguyen, Liang Song, José M. Alvarez, Shao-Shan Huang, Huaming Chen, Niroshan Ramachandran, Stefan Altmann, Rodrigo A. Gutiérrez, David E. Hill, Julian I. Schroeder, Joanne Chory, Joshua LaBaerMarc Vidal, Pascal Braun, Joseph R. Ecker

Research output: Contribution to journalArticle

Abstract

Protein microarrays enable investigation of diverse biochemical properties for thousands of proteins in a single experiment, an unparalleled capacity. Using a high-density system called HaloTag nucleic acid programmable protein array (HaloTag-NAPPA), we created high-density protein arrays comprising 12,000 Arabidopsis ORFs. We used these arrays to query protein-protein interactions for a set of 38 transcription factors and transcriptional regulators (TFs) that function in diverse plant hormone regulatory pathways. The resulting transcription factor interactome network, TF-NAPPA, contains thousands of novel interactions. Validation in a benchmarked in vitro pull-down assay revealed that a random subset of TF-NAPPA validated at the same rate of 64% as a positive reference set of literaturecurated interactions. Moreover, using a bimolecular fluorescence complementation (BiFC) assay, we confirmed in planta several interactions of biological interest and determined the interaction localizations for seven pairs. The application of HaloTag-NAPPA technology to plant hormone signaling pathways allowed the identification of many novel transcription factor-protein interactions and led to the development of a proteome-wide plant hormone TF interactome network.

Original languageEnglish (US)
Pages (from-to)E4238-E4247
JournalProceedings of the National Academy of Sciences of the United States of America
Volume113
Issue number29
DOIs
StatePublished - Jul 19 2016

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Protein Array Analysis
Plant Growth Regulators
Transcription Factors
Nucleic Acids
Proteins
Proteome
Arabidopsis
Open Reading Frames
Fluorescence
Technology

Keywords

  • Arabidopsis thaliana
  • Hormone
  • Interactome
  • Protein arrays
  • Systems biology

ASJC Scopus subject areas

  • General

Cite this

Mapping transcription factor interactome networks using HaloTag protein arrays. / Yazaki, Junshi; Galli, Mary; Kim, Alice Y.; Nito, Kazumasa; Aleman, Fernando; Chang, Katherine N.; Carvunis, Anne Ruxandra; Quan, Rosa; Nguyen, Hien; Song, Liang; Alvarez, José M.; Huang, Shao-Shan; Chen, Huaming; Ramachandran, Niroshan; Altmann, Stefan; Gutiérrez, Rodrigo A.; Hill, David E.; Schroeder, Julian I.; Chory, Joanne; LaBaer, Joshua; Vidal, Marc; Braun, Pascal; Ecker, Joseph R.

In: Proceedings of the National Academy of Sciences of the United States of America, Vol. 113, No. 29, 19.07.2016, p. E4238-E4247.

Research output: Contribution to journalArticle

Yazaki, J, Galli, M, Kim, AY, Nito, K, Aleman, F, Chang, KN, Carvunis, AR, Quan, R, Nguyen, H, Song, L, Alvarez, JM, Huang, S-S, Chen, H, Ramachandran, N, Altmann, S, Gutiérrez, RA, Hill, DE, Schroeder, JI, Chory, J, LaBaer, J, Vidal, M, Braun, P & Ecker, JR 2016, 'Mapping transcription factor interactome networks using HaloTag protein arrays', Proceedings of the National Academy of Sciences of the United States of America, vol. 113, no. 29, pp. E4238-E4247. https://doi.org/10.1073/pnas.1603229113
Yazaki, Junshi ; Galli, Mary ; Kim, Alice Y. ; Nito, Kazumasa ; Aleman, Fernando ; Chang, Katherine N. ; Carvunis, Anne Ruxandra ; Quan, Rosa ; Nguyen, Hien ; Song, Liang ; Alvarez, José M. ; Huang, Shao-Shan ; Chen, Huaming ; Ramachandran, Niroshan ; Altmann, Stefan ; Gutiérrez, Rodrigo A. ; Hill, David E. ; Schroeder, Julian I. ; Chory, Joanne ; LaBaer, Joshua ; Vidal, Marc ; Braun, Pascal ; Ecker, Joseph R. / Mapping transcription factor interactome networks using HaloTag protein arrays. In: Proceedings of the National Academy of Sciences of the United States of America. 2016 ; Vol. 113, No. 29. pp. E4238-E4247.
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