Temporal transcriptional response to ethylene gas drives growth hormone cross-regulation in Arabidopsis
Katherine Noelani Chang,
Shan Zhong,
Matthew T Weirauch,
Gary Hon,
Mattia Pelizzola,
Hai Li,
Shao-shan Carol Huang,
Robert J Schmitz,
Mark A Urich,
Dwight Kuo,
Joseph R Nery,
Hong Qiao,
Ally Yang,
Abdullah Jamali,
Huaming Chen,
Trey Ideker,
Bing Ren,
Ziv Bar-Joseph,
Timothy R Hughes,
Joseph R Ecker
Affiliations
Katherine Noelani Chang
Plant Biology Laboratory, and Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, United States
Shan Zhong
Lane Center for Computational Biology, School of Computer Science, Carnegie Mellon University, Pittsburgh, United States
Matthew T Weirauch
Department of Molecular Genetics and Banting and Best Department of Medical Research, University of Toronto, Ontario, Canada
Gary Hon
Ludwig Institute for Cancer Research, University of California, San Diego, La Jolla, United States
Mattia Pelizzola
Plant Biology Laboratory, and Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, United States
Hai Li
Plant Biology Laboratory, and Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, United States
Shao-shan Carol Huang
Plant Biology Laboratory, and Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, United States; Howard Hughes Medical Institute, The Salk Institute for Biological Studies, La Jolla, United States
Robert J Schmitz
Plant Biology Laboratory, and Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, United States
Mark A Urich
Plant Biology Laboratory, and Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, United States
Dwight Kuo
Department of Bioengineering, Department of Medicine, The Institute for Genomic Medicine, University of California, San Diego, La Jolla, United States
Joseph R Nery
Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, United States
Hong Qiao
Plant Biology Laboratory, and Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, United States
Ally Yang
Department of Molecular Genetics and Banting and Best Department of Medical Research, University of Toronto, Ontario, Canada
Abdullah Jamali
Plant Biology Laboratory, and Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, United States
Huaming Chen
Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, United States
Trey Ideker
Departments of Medicine and Bioengineering, University of California, San Diego, San Diego, United States
Bing Ren
Ludwig Institute for Cancer Research, University of California, San Diego, La Jolla, United States; Department of Cellular and Molecular Medicine, University of California, San Diego School of Medicine, San Diego, United States
Ziv Bar-Joseph
Lane Center for Computational Biology, School of Computer Science, Carnegie Mellon University, Pittsburgh, United States; Machine Learning Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, United States
Timothy R Hughes
Department of Molecular Genetics and Banting and Best Department of Medical Research, University of Toronto, Ontario, Canada
Joseph R Ecker
Plant Biology Laboratory, and Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, United States; Howard Hughes Medical Institute, The Salk Institute for Biological Studies, La Jolla, United States
The gaseous plant hormone ethylene regulates a multitude of growth and developmental processes. How the numerous growth control pathways are coordinated by the ethylene transcriptional response remains elusive. We characterized the dynamic ethylene transcriptional response by identifying targets of the master regulator of the ethylene signaling pathway, ETHYLENE INSENSITIVE3 (EIN3), using chromatin immunoprecipitation sequencing and transcript sequencing during a timecourse of ethylene treatment. Ethylene-induced transcription occurs in temporal waves regulated by EIN3, suggesting distinct layers of transcriptional control. EIN3 binding was found to modulate a multitude of downstream transcriptional cascades, including a major feedback regulatory circuitry of the ethylene signaling pathway, as well as integrating numerous connections between most of the hormone mediated growth response pathways. These findings provide direct evidence linking each of the major plant growth and development networks in novel ways.
