ARS | Publication request: A stele-enriched gene regulatory network in the arabidopsis root

Submitted to: EMBO Journal
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: November 17, 2010
Publication Date: January 18, 2011
Citation: Brady, S.M., Zhang, L., Megraw, M., Martinez, N.J., Jiang, E., Yi, C.S., Ware, D., Walhout, A.J., Benfey, P.N. 2011. A stele-enriched gene regulatory network in the arabidopsis root. EMBO Journal. 7:459.

Interpretive Summary: In multicellular organisms like plants, expression of genes is under complex regulation. The complex regulation controls, when, where and how much the gene is expressed. A great deal of the control of this regulation is due to two classes of genes; transcription factors (TF) and microRNAs (miRNA). Transcription factors are protein coding genes that bind to the promoters of gene, to promote or repress transcriptions in a spatially restricted manner. MicroRNAs are a class of non-coding genes that can further refine the spatial expression of these transcription factors. In this manuscript, we have used the combination of experimental approaches that allow us to identify within specific cell types the interaction between transcription factors and miRNAs to establish a gene regulatory network (GRN) of transcription factors and miRNA expression in roots. This network consisting of 103 interactions between 64 TFs and 8 miRNAs, and is the largest network in its type in plants. The data had been validated within the plant using several experimental techniques. Our data provides an understanding of the regulatory complexity in the root stele. This information can be used by breeders inform candidate genes involved in root development, as well as in the selection on the choice of promoters (native rather than artificial) to alternate the gene expression levels in the root.

Technical Abstract: Tightly controlled gene expression is a hallmark of multicellular development and is accomplished by transcription factors (TFs) and microRNAs (miRNAs). While many studies have focused on identifying downstream targets of these molecules, less is known about the factors that regulate their differential expression. We used high spatial resolution gene expression data with yeast one-hybrid (Y1H) and two-hybrid (Y2H) assays to delineate the first tissue-specific gene regulatory network (GRN) of 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. Using modeling, we predicted the regulatory consequence of each TF for its target. Remarkably, molecular phenotypes were identified for 65% of the TFs, but morphological phenotypes were associated with only 16%. This indicates that gene redundancy does not solely occur at the level of gene regulation, and that gene expression changes may be canalized or buffered.