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Title: Temporal transcriptional response to ethylene gas drives growth hormone cross-regulation in Arabidopsis

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.
Authors:
 [1] ;  [2] ;  [3] ;  [4] ;  [1] ;  [1] ;  [5] ;  [1] ;  [1] ;  [6] ;  [7] ;  [1] ;  [3] ;  [1] ;  [7] ;  [8] ;  [9] ;  [10] ;  [3] ;  [5]
  1. Plant Biology Laboratory, and Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, United States
  2. Lane Center for Computational Biology, School of Computer Science, Carnegie Mellon University, Pittsburgh, United States
  3. Department of Molecular Genetics and Banting and Best Department of Medical Research, University of Toronto, Ontario, Canada
  4. Ludwig Institute for Cancer Research, University of California, San Diego, La Jolla, United States
  5. 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
  6. Department of Bioengineering, Department of Medicine, The Institute for Genomic Medicine, University of California, San Diego, La Jolla, United States
  7. Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, United States
  8. Departments of Medicine and Bioengineering, University of California, San Diego, San Diego, United States
  9. 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
  10. 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
Publication Date:
Grant/Contract Number:
FG03-00ER15113, DE-FG02-04ER15517
Type:
Published Article
Journal Name:
eLife
Additional Journal Information:
Journal Name: eLife Journal Volume: 2; Journal ID: ISSN 2050-084X
Publisher:
eLife Sciences Publications, Ltd.
Sponsoring Org:
USDOE
Country of Publication:
United States
Language:
English
OSTI Identifier:
1197659
Alternate Identifier(s):
OSTI ID: 1197660

Chang, Katherine Noelani, Zhong, Shan, Weirauch, Matthew T., Hon, Gary, Pelizzola, Mattia, Li, Hai, Huang, Shao-shan Carol, Schmitz, Robert J., Urich, Mark A., Kuo, Dwight, Nery, Joseph R., Qiao, Hong, Yang, Ally, Jamali, Abdullah, Chen, Huaming, Ideker, Trey, Ren, Bing, Bar-Joseph, Ziv, Hughes, Timothy R., and Ecker, Joseph R.. Temporal transcriptional response to ethylene gas drives growth hormone cross-regulation in Arabidopsis. United States: N. p., Web. doi:10.7554/eLife.00675.
Chang, Katherine Noelani, Zhong, Shan, Weirauch, Matthew T., Hon, Gary, Pelizzola, Mattia, Li, Hai, Huang, Shao-shan Carol, Schmitz, Robert J., Urich, Mark A., Kuo, Dwight, Nery, Joseph R., Qiao, Hong, Yang, Ally, Jamali, Abdullah, Chen, Huaming, Ideker, Trey, Ren, Bing, Bar-Joseph, Ziv, Hughes, Timothy R., & Ecker, Joseph R.. Temporal transcriptional response to ethylene gas drives growth hormone cross-regulation in Arabidopsis. United States. doi:10.7554/eLife.00675.
Chang, Katherine Noelani, Zhong, Shan, Weirauch, Matthew T., Hon, Gary, Pelizzola, Mattia, Li, Hai, Huang, Shao-shan Carol, Schmitz, Robert J., Urich, Mark A., Kuo, Dwight, Nery, Joseph R., Qiao, Hong, Yang, Ally, Jamali, Abdullah, Chen, Huaming, Ideker, Trey, Ren, Bing, Bar-Joseph, Ziv, Hughes, Timothy R., and Ecker, Joseph R.. 2013. "Temporal transcriptional response to ethylene gas drives growth hormone cross-regulation in Arabidopsis". United States. doi:10.7554/eLife.00675.
@article{osti_1197659,
title = {Temporal transcriptional response to ethylene gas drives growth hormone cross-regulation in Arabidopsis},
author = {Chang, Katherine Noelani and Zhong, Shan and Weirauch, Matthew T. and Hon, Gary and Pelizzola, Mattia and Li, Hai and Huang, Shao-shan Carol and Schmitz, Robert J. and Urich, Mark A. and Kuo, Dwight and Nery, Joseph R. and Qiao, Hong and Yang, Ally and Jamali, Abdullah and Chen, Huaming and Ideker, Trey and Ren, Bing and Bar-Joseph, Ziv and Hughes, Timothy R. and Ecker, Joseph R.},
abstractNote = {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.},
doi = {10.7554/eLife.00675},
journal = {eLife},
number = ,
volume = 2,
place = {United States},
year = {2013},
month = {6}
}

Works referenced in this record:

Genome-Wide Insertional Mutagenesis of Arabidopsis thaliana
journal, August 2003
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Plant Responses to Ethylene Gas Are Mediated by SCFEBF1/EBF2-Dependent Proteolysis of EIN3 Transcription Factor
journal, December 2003

Activation of the Ethylene Gas Response Pathway in Arabidopsis by the Nuclear Protein ETHYLENE-INSENSITIVE3 and Related Proteins
journal, June 1997