title: Mapping transcription factor interactome networks using HaloTag protein arrays.
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 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.
authors.affiliation: Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037; Plant Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037; RIKEN Center for Integrative Medical Sciences, Yokohama City, Kanagawa 230-0045, Japan;
authors.forename: Junshi
authors.initials: J
authors.lastname: Yazaki
authors.affiliation: Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037;
authors.forename: Mary
authors.initials: M
authors.lastname: Galli
authors.affiliation: Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037;
authors.forename: Alice Y
authors.initials: AY
authors.lastname: Kim
authors.affiliation: Plant Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037;
authors.forename: Kazumasa
authors.initials: K
authors.lastname: Nito
authors.affiliation: Cell and Developmental Biology Section, Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093;
authors.forename: Fernando
authors.initials: F
authors.lastname: Aleman
authors.affiliation: Plant Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037;
authors.forename: Katherine N
authors.initials: KN
authors.lastname: Chang
authors.affiliation: Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA 02215; Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215; Department of Genetics, Harvard Medical School, Boston, MA 02115;
authors.forename: Anne-Ruxandra
authors.identifier: 0000-0002-6474-6413
authors.initials: AR
authors.lastname: Carvunis
authors.affiliation: Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037;
authors.forename: Rosa
authors.initials: R
authors.lastname: Quan
authors.affiliation: Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037;
authors.forename: Hien
authors.initials: H
authors.lastname: Nguyen
authors.affiliation: Plant Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037;
authors.forename: Liang
authors.initials: L
authors.lastname: Song
authors.affiliation: Fondo de Financiamiento de Centros de Investigación en Áreas Prioritarias (FONDAP) Center for Genome Regulation, Millennium Nucleus Center for Plant Systems and Synthetic Biology, Departamento de Genética Molecular y Microbiología, Pontificia Universidad Católica de Chile, 340 Santiago, Chile;
authors.forename: José M
authors.initials: JM
authors.lastname: Alvarez
authors.affiliation: Plant Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037;
authors.forename: Shao-Shan Carol
authors.initials: SS
authors.lastname: Huang
authors.affiliation: Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037;
authors.forename: Huaming
authors.initials: H
authors.lastname: Chen
authors.affiliation: Life Technologies, Carlsbad, CA 92008;
authors.forename: Niroshan
authors.initials: N
authors.lastname: Ramachandran
authors.affiliation: Plant Systems Biology, School of Life Sciences Weihenstephan (WZW), Technische Universität München (TUM), 85354 Freising, Germany;
authors.forename: Stefan
authors.initials: S
authors.lastname: Altmann
authors.affiliation: Fondo de Financiamiento de Centros de Investigación en Áreas Prioritarias (FONDAP) Center for Genome Regulation, Millennium Nucleus Center for Plant Systems and Synthetic Biology, Departamento de Genética Molecular y Microbiología, Pontificia Universidad Católica de Chile, 340 Santiago, Chile;
authors.forename: Rodrigo A
authors.initials: RA
authors.lastname: Gutiérrez
authors.affiliation: Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA 02215; Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215; Department of Genetics, Harvard Medical School, Boston, MA 02115;
authors.forename: David E
authors.identifier: 0000-0001-5192-0921
authors.initials: DE
authors.lastname: Hill
authors.affiliation: Cell and Developmental Biology Section, Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093;
authors.forename: Julian I
authors.initials: JI
authors.lastname: Schroeder
authors.affiliation: Plant Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037; Howard Hughes Medical Institute, The Salk Institute for Biological Studies, La Jolla, CA 92037;
authors.forename: Joanne
authors.initials: J
authors.lastname: Chory
authors.affiliation: Personalized Diagnostics, The Biodesign Institute, Arizona State University, Tempe, AZ 85287;
authors.forename: Joshua
authors.initials: J
authors.lastname: LaBaer
authors.affiliation: Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA 02215; Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215; Department of Genetics, Harvard Medical School, Boston, MA 02115;
authors.forename: Marc
authors.initials: M
authors.lastname: Vidal
authors.affiliation: Plant Systems Biology, School of Life Sciences Weihenstephan (WZW), Technische Universität München (TUM), 85354 Freising, Germany; Institute for Advanced Study, Technische Universität München (TUM), 85748 Garching, Germany pbraun@wzw.tum.de ecker@salk.edu.
authors.forename: Pascal
authors.initials: P
authors.lastname: Braun
authors.affiliation: Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037; Plant Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037; Howard Hughes Medical Institute, The Salk Institute for Biological Studies, La Jolla, CA 92037; pbraun@wzw.tum.de ecker@salk.edu.
authors.forename: Joseph R
authors.initials: JR
authors.lastname: Ecker
mesh_terms: D017360:Arabidopsis / Q000378:metabolism; D029681:Arabidopsis Proteins / Q000378:metabolism*; D010937:Plant Growth Regulators / Q000378:metabolism*; D040081:Protein Array Analysis; D025941:Protein Interaction Mapping; D014157:Transcription Factors / Q000378:metabolism*
chemical_list: D029681:Arabidopsis Proteins; D010937:Plant Growth Regulators; D014157:Transcription Factors
keywords: Arabidopsis thaliana; hormone; interactome; protein arrays; systems biology