Open AccessA stele‐enriched gene regulatory network in the Arabidopsis root
Author(s) -
Brady Siobhan M,
Zhang Lifang,
Megraw Molly,
Martinez Natalia J,
Jiang Eric,
Yi Charles S,
Liu Weilin,
Zeng Anna,
TaylorTeeples Mallorie,
Kim Dahae,
Ahnert Sebastian,
Ohler Uwe,
Ware Doreen,
Walhout Albertha J M,
Benfey Philip N
Publication year - 2011
Publication title -
molecular systems biology
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 8.523
H-Index - 148
ISSN - 1744-4292
DOI - 10.1038/msb.2010.114
Subject(s) - biology , gene regulatory network , arabidopsis , regulation of gene expression , microrna , multicellular organism , gene , gene expression , genetics , transcription factor , phenotype , computational biology , promoter , regulatory sequence , regulator gene , microbiology and biotechnology , mutant
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.