A transcription factor hierarchy defines an environmental stress response network.
Environmental stresses are universally encountered by microbes, plants, and animals. Yet systematic studies of stress-responsive transcription factor (TF) networks in multicellular organisms have been limited. The phytohormone abscisic acid (ABA) influences the expression of thousands of genes, allowing us to characterize complex stress-responsive regulatory networks. Using chromatin immunoprecipitation sequencing, we identified genome-wide targets of 21 ABA-related TFs to construct a comprehensive regulatory network in Arabidopsis thaliana Determinants of dynamic TF binding and a hierarchy among TFs were defined, illuminating the relationship between differential gene expression patterns and ABA pathway feedback regulation. By extrapolating regulatory characteristics of observed canonical ABA pathway components, we identified a new family of transcriptional regulators modulating ABA and salt responsiveness and demonstrated their utility to modulate plant resilience to osmotic stress.
Plant Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA.
Liang
L
Song
Plant Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA.
Shao-Shan Carol
SC
Huang
Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA 15213, USA.
Aaron
A
Wise
Genomic Analysis Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA.
Rosa
R
Castanon
Genomic Analysis Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA.
Joseph R
JR
Nery
Genomic Analysis Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA.
Huaming
H
Chen
Plant Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA.
Marina
M
Watanabe
Plant Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA.
Jerushah
J
Thomas
Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA 15213, USA.
Ziv
Z
Bar-Joseph
Plant Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA. ecker@salk.edu.|Genomic Analysis Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA.|Howard Hughes Medical Institute (HHMI), Salk Institute for Biological Studies, La Jolla, CA 92037, USA.
Joseph R
JR
Ecker
D000040:Abscisic Acid / Q000378:metabolism / Q000494:pharmacology; D017360:Arabidopsis / Q000187:drug effects / Q000235:genetics* / Q000502:physiology*; D029681:Arabidopsis Proteins / Q000145:classification / Q000235:genetics / Q000378:metabolism; D001665:Binding Sites; D047369:Chromatin Immunoprecipitation; D018744:DNA, Plant / Q000378:metabolism; D055864:Droughts; D018506:Gene Expression Regulation, Plant / Q000187:drug effects; D009997:Osmotic Pressure; D010937:Plant Growth Regulators / Q000378:metabolism / Q000494:pharmacology; D011485:Protein Binding; D054712:Salinity; D017422:Sequence Analysis, DNA; D013312:Stress, Physiological / Q000235:genetics*; D049490:Systems Biology; D014157:Transcription Factors / Q000145:classification / Q000235:genetics / Q000378:metabolism; D014867:Water / Q000502:physiology*
D029681:Arabidopsis Proteins; D018744:DNA, Plant; D010937:Plant Growth Regulators; D014157:Transcription Factors; D014867:Water; D000040:Abscisic Acid