Program in Gene Function and Expression; Program in Molecular Medicine
Medical Subject Headings
Arabidopsis; Arabidopsis Proteins; Gene Expression Profiling; Gene Regulatory Networks; MicroRNAs; Plant Roots; Reproducibility of Results; Systems Biology; Transcription Factors; Two-Hybrid System Techniques
Genetics and Genomics
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.
Rights and Permissions
Citation: Mol Syst Biol. 2011 Jan 18;7:459. Link to article on publisher's site This is an open-access article distributed under the terms of the Creative Commons Attribution Noncommercial Share Alike 3.0 Unported License, which allows readers to alter, transform, or build upon the article and then distribute the resulting work under the same or similar license to this one. The work must be attributed back to the original author and commercial use is not permitted without specific permission.
Brady, Siobhan M.; Zhang, Lifang; Megraw, Molly; Martinez, Natalia Julia; Jiang, Eric; Yi, Charles S.; Liu, Weilin; Zeng, Anna; Taylor-Teeples, Mallorie; Kim, Dahae; Ahnert, Sebastian; Ohler, Uwe; Ware, Doreen; Walhout, Albertha J. M.; and Benfey, Philip N., "A stele-enriched gene regulatory network in the Arabidopsis root" (2011). Program in Gene Function and Expression Publications and Presentations. 170.