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

Journal Article · · eLife
DOI:https://doi.org/10.7554/eLife.00675· OSTI ID:1197659
 [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

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.

Research Organization:
Salk Institute for Biological Studies, La Jolla, CA (United States)
Sponsoring Organization:
USDOE Office of Science (SC), Biological and Environmental Research (BER). Biological Systems Science Division
Grant/Contract Number:
FG03-00ER15113, DE-FG02-04ER15517; MCB-0924871; FG02-04ER15517; FG03-00ER15113
OSTI ID:
1197659
Alternate ID(s):
OSTI ID: 1197660; OSTI ID: 1628795
Journal Information:
eLife, Journal Name: eLife Vol. 2; ISSN 2050-084X
Publisher:
eLife Sciences Publications, Ltd.Copyright Statement
Country of Publication:
United States
Language:
English
Citation Metrics:
Cited by: 285 works
Citation information provided by
Web of Science

References (73)

A New Class of Arabidopsis Constitutive Photomorphogenic Genes Involved in Regulating Cotyledon Development. journal March 1993
Multiple sequence alignment with the Clustal series of programs journal July 2003
FLOWERING LOCUS C (FLC) regulates development pathways throughout the life cycle of Arabidopsis journal April 2011
Model-based Analysis of ChIP-Seq (MACS) journal January 2008
Ethylene in vegetative development: a tale with a riddle: Tansley review journal March 2012
Genome-Wide Insertional Mutagenesis of Arabidopsis thaliana journal August 2003
Direct transcriptional control of the Arabidopsis immune receptor FLS2 by the ethylene-dependent transcription factors EIN3 and EIL1 journal July 2010
Variation in Homeodomain DNA Binding Revealed by High-Resolution Analysis of Sequence Preferences journal June 2008
Arabidopsis Seedling Growth Response and Recovery to Ethylene. A Kinetic Analysis journal October 2004
Negative Autoregulation Speeds the Response Times of Transcription Networks journal November 2002
Design and analysis of ChIP-seq experiments for DNA-binding proteins journal November 2008
Sequence specificity is obtained from the majority of modular C2H2 zinc-finger arrays journal February 2011
Ethylene inhibits lateral root development, increases IAA transport and expression of PIN3 and PIN7 auxin efflux carriers journal July 2011
Dynamic and complex transcription factor binding during an inducible response in yeast journal June 2009
Feedback regulation of EGFR signalling: decision making by early and delayed loops journal January 2011
Integration of Brassinosteroid Signal Transduction with the Transcription Network for Plant Growth Regulation in Arabidopsis journal November 2010
Derepression of ethylene-stabilized transcription factors (EIN3/EIL1) mediates jasmonate and ethylene signaling synergy in Arabidopsis journal July 2011
Profiling DNA methylation patterns using genomic tiling microarrays journal March 2005
Impulse Control: Temporal Dynamics in Gene Transcription journal March 2011
The SOX2 response program in glioblastoma multiforme: an integrated ChIP-seq, expression microarray, and microRNA analysis journal January 2011
Genome-wide protein–DNA binding dynamics suggest a molecular clutch for transcription factor function journal April 2012
HOOKLESS1, an Ethylene Response Gene, Is Required for Differential Cell Elongation in the Arabidopsis Hypocotyl journal April 1996
A brassinosteroid transcriptional network revealed by genome-wide identification of BESI target genes in Arabidopsis thaliana: Brassinosteroid transcriptional network journal January 2011
Nascent-Seq reveals novel features of mouse circadian transcriptional regulation journal November 2012
PeakSeq enables systematic scoring of ChIP-seq experiments relative to controls journal January 2009
Short-Term Growth Responses to Ethylene in Arabidopsis Seedlings Are EIN3/EIL1 Independent journal October 2004
Genome-wide transcription factor binding: beyond direct target regulation journal April 2011
LEAFY Target Genes Reveal Floral Regulatory Logic, cis Motifs, and a Link to Biotic Stimulus Response journal April 2011
Development of Arabidopsis whole-genome microarrays and their application to the discovery of binding sites for the TGA2 transcription factor in salicylic acid-treated plants journal July 2006
Identifying DNA and protein patterns with statistically significant alignments of multiple sequences journal July 1999
Evidence for Network Evolution in an Arabidopsis Interactome Map journal July 2011
Orchestration of Floral Initiation by APETALA1 journal April 2010
Plant Responses to Ethylene Gas Are Mediated by SCFEBF1/EBF2-Dependent Proteolysis of EIN3 Transcription Factor journal December 2003
Arabidopsis Hormone Database: a comprehensive genetic and phenotypic information database for plant hormone research in Arabidopsis journal November 2008
Ethylene signaling: new levels of complexity and regulation journal October 2008
Quantitative analysis demonstrates most transcription factors require only simple models of specificity journal June 2011
Diversity and Complexity in DNA Recognition by Transcription Factors journal May 2009
The Regulation of Aging and Longevity: A New and Complex Role of p53 journal April 2011
Statistical mechanical modeling of genome-wide transcription factor occupancy data by MatrixREDUCE journal July 2006
Convergence of Signaling Pathways in the Control of Differential Cell Growth in Arabidopsis journal August 2004
Nuclear events in ethylene signaling: a transcriptional cascade mediated by ETHYLENE-INSENSITIVE3 and ETHYLENE-RESPONSE-FACTOR1 journal December 1998
Five components of the ethylene-response pathway identified in a screen for weak ethylene-insensitive mutants in Arabidopsis journal February 2003
AGRIS: the Arabidopsis Gene Regulatory Information Server, an update journal November 2010
ETHYLENE INSENSITIVE3 and ETHYLENE INSENSITIVE3-LIKE1 Repress SALICYLIC ACID INDUCTION DEFICIENT2 Expression to Negatively Regulate Plant Innate Immunity in Arabidopsis journal August 2009
Auxin, Ethylene and Brassinosteroids: Tripartite Control of Growth in the Arabidopsis Hypocotyl journal June 2005
A new Generation of Homology Search Tools Based on Probabilistic Inference conference March 2012
Cytoscape: A Software Environment for Integrated Models of Biomolecular Interaction Networks journal November 2003
Orchestration of the Floral Transition and Floral Development in Arabidopsis by the Bifunctional Transcription Factor APETALA2 journal July 2010
Localization of the Raf-like Kinase CTR1 to the Endoplasmic Reticulum of Arabidopsis through Participation in Ethylene Receptor Signaling Complexes journal June 2003
Cloning and DNA-binding properties of a tobacco Ethylene-Insensitive3 (EIN3) homolog journal February 2000
The embryonic leaf identity gene FUSCA3 regulates vegetative phase transitions by negatively modulating ethylene-regulated gene expression in Arabidopsis journal January 2012
EIN3/EIL1 cooperate with PIF1 to prevent photo-oxidation and to promote greening of Arabidopsis seedlings journal November 2009
Reconstructing dynamic regulatory maps journal January 2007
Target Genes of the MADS Transcription Factor SEPALLATA3: Integration of Developmental and Hormonal Pathways in the Arabidopsis Flower journal April 2009
Universal protein-binding microarrays for the comprehensive characterization of the DNA-binding specificities of transcription factors journal March 2009
Characterization of SOC1’s Central Role in Flowering by the Identification of Its Upstream and Downstream Regulators journal July 2012
MicroRNA-Mediated Feedback and Feedforward Loops Are Recurrent Network Motifs in Mammals journal June 2007
Involvement of HLS1 in Sugar and Auxin Signaling in Arabidopsis Leaves journal December 2006
Compact, universal DNA microarrays to comprehensively determine transcription-factor binding site specificities journal September 2006
The Pfam protein families database journal November 2009
BiNGO: a Cytoscape plugin to assess overrepresentation of Gene Ontology categories in Biological Networks journal June 2005
STAMP: a web tool for exploring DNA-binding motif similarities journal May 2007
Different Plant Hormones Regulate Similar Processes through Largely Nonoverlapping Transcriptional Responses journal August 2006
A module of negative feedback regulators defines growth factor signaling journal February 2007
Changes in 5S rDNA Chromatin Organization and Transcription during Heterochromatin Establishment in Arabidopsis journal November 2003
Arabidopsis auxin-resistance gene AXR1 encodes a protein related to ubiquitin-activating enzyme E1 journal July 1993
Highly Integrated Single-Base Resolution Maps of the Epigenome in Arabidopsis journal May 2008
Combinatorial binding predicts spatio-temporal cis-regulatory activity journal November 2009
Improved detection of DNA motifs using a self-organized clustering of familial binding profiles journal June 2005
Activation of the Ethylene Gas Response Pathway in Arabidopsis by the Nuclear Protein ETHYLENE-INSENSITIVE3 and Related Proteins journal June 1997
Ethylene signaling in Arabidopsis involves feedback regulation via the elaborate control of EBF2 expression by EIN3 journal September 2008
Cell Identity Regulators Link Development and Stress Responses in the Arabidopsis Root journal October 2011
Temporal and Spatial Changes in Transcription Factor Binding and Histone Modifications at the Steroidogenic Acute Regulatory Protein ( StAR ) Locus Associated with StAR Transcription journal April 2004

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