Mapping transcription factor interactome networks using HaloTag protein arrays

Proc Natl Acad Sci U S A. 2016 Jul 19;113(29):E4238-47. doi: 10.1073/pnas.1603229113. Epub 2016 Jun 29.


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 literature-curated 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.

Keywords: Arabidopsis thaliana; hormone; interactome; protein arrays; systems biology.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Arabidopsis / metabolism
  • Arabidopsis Proteins / metabolism*
  • Plant Growth Regulators / metabolism*
  • Protein Array Analysis
  • Protein Interaction Mapping
  • Transcription Factors / metabolism*


  • Arabidopsis Proteins
  • Plant Growth Regulators
  • Transcription Factors