A stele-enriched gene regulatory network in the Arabidopsis root.

TitleA stele-enriched gene regulatory network in the Arabidopsis root.
Publication TypeJournal Article
Year of Publication2011
AuthorsBrady, SM, Zhang, L, Megraw, M, Martinez, NJ, Jiang, E, Yi, CS, Liu, W, Zeng, A, Taylor-Teeples, M, Kim, D, Ahnert, S, Ohler, U, Ware, D, Walhout, AJM, Benfey, PN
JournalMol Syst Biol
Date Published2011 Jan 18
KeywordsArabidopsis, Arabidopsis Proteins, Gene Expression Profiling, Gene Regulatory Networks, MicroRNAs, Plant Roots, Reproducibility of Results, Systems Biology, Transcription Factors, Two-Hybrid System Techniques

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.

Alternate JournalMol. Syst. Biol.
PubMed ID21245844
PubMed Central IDPMC3049412
Grant ListDK068429 / DK / NIDDK NIH HHS / United States
GM082971 / GM / NIGMS NIH HHS / United States
R01 DK068429 / DK / NIDDK NIH HHS / United States