A stele-enriched gene regulatory network in the Arabidopsis root.
Tightly controlled gene expression is a hallmark of multicellular development and is accomplished by transcription factors (TFs) and microRNAs (miRNAs). Although many studies have focused on identifying downstream targets of these molecules, less is known about the factors that regulate their differential expression. We used data from high spatial resolution gene expression experiments and yeast one-hybrid (Y1H) and two-hybrid (Y2H) assays to delineate a subset of interactions occurring within a gene regulatory network (GRN) that determines tissue-specific TF and miRNA expression in plants. We find that upstream TFs are expressed in more diverse cell types than their targets and that promoters that are bound by a relatively large number of TFs correspond to key developmental regulators. The regulatory consequence of many TFs for their target was experimentally determined using genetic analysis. Remarkably, molecular phenotypes were identified for 65% of the TFs, but morphological phenotypes were associated with only 16%. This indicates that the GRN is robust, and that gene expression changes may be canalized or buffered.
Department of Biology and IGSP Center for Systems Biology, Duke University, Durham, NC 27708, USA.
Siobhan M
SM
Brady
Lifang
L
Zhang
Molly
M
Megraw
Natalia J
NJ
Martinez
Eric
E
Jiang
Charles S
CS
Yi
Weilin
W
Liu
Anna
A
Zeng
Mallorie
M
Taylor-Teeples
Dahae
D
Kim
Sebastian
S
Ahnert
Uwe
U
Ohler
Doreen
D
Ware
Albertha J M
AJ
Walhout
Philip N
PN
Benfey
D017360:Arabidopsis / Q000235:genetics* / Q000502:physiology; D029681:Arabidopsis Proteins / Q000235:genetics* / Q000378:metabolism; D020869:Gene Expression Profiling; D053263:Gene Regulatory Networks / Q000502:physiology*; D035683:MicroRNAs / Q000235:genetics / Q000378:metabolism; D018517:Plant Roots / Q000502:physiology; D015203:Reproducibility of Results; D049490:Systems Biology / Q000379:methods*; D014157:Transcription Factors / Q000235:genetics / Q000378:metabolism; D020798:Two-Hybrid System Techniques
D029681:Arabidopsis Proteins; D035683:MicroRNAs; D014157:Transcription Factors
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