Program in Gene Function and Expression; Program in Molecular Medicine
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.
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DOI of Published Version
Mol Syst Biol. 2011 Jan 18;7:459. Link to article on publisher's site
Molecular systems biology
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.