Establishment of Expression in the SHORTROOT-SCARECROW Transcriptional Cascade through Opposing Activities of Both Activators and Repressors

• Published in: Developmental cell Vol. 39; no. 5; pp. 585 - 596
• Main Authors: Sparks, Erin E., Drapek, Colleen, Gaudinier, Allison, Li, Song, Ansariola, Mitra, Shen, Ning, Hennacy, Jessica H., Zhang, Jingyuan, Turco, Gina, Petricka, Jalean J., Foret, Jessica, Hartemink, Alexander J., Gordân, Raluca, Megraw, Molly, Brady, Siobhan M., Benfey, Philip N.
• Format: Journal Article
• Language: English
• Published: United States Elsevier Inc 05.12.2016
• Subjects: Arabidopsis; Arabidopsis - genetics; Arabidopsis - growth & development; Arabidopsis - metabolism; Arabidopsis Proteins - genetics; Arabidopsis Proteins - metabolism; Computer Simulation; Gene Expression Regulation, Plant; Gene Regulatory Networks; Genes, Plant; Genes, Reporter; Genes, Synthetic; Models, Genetic; Plant Roots - cytology; Plant Roots - metabolism; Plants, Genetically Modified; Promoter Regions, Genetic; Repressor Proteins - genetics; Repressor Proteins - metabolism; roots; SCARECROW; SHORTROOT; Trans-Activators - genetics; Trans-Activators - metabolism; transcription factor; Transcription Factors - genetics; Transcription Factors - metabolism; Two-Hybrid System Techniques; transcription factor; SHORTROOT; roots; Arabidopsis; SCARECROW
• ISSN: 1534-5807; 1878-1551
• DOI: 10.1016/j.devcel.2016.09.031

Tissue-specific gene expression is often thought to arise from spatially restricted transcriptional cascades. However, it is unclear how expression is established at the top of these cascades in the absence of pre-existing specificity. We generated a transcriptional network to explore how transcription factor expression is established in the Arabidopsis thaliana root ground tissue. Regulators of the SHORTROOT-SCARECROW transcriptional cascade were validated in planta. At the top of this cascade, we identified both activators and repressors of SHORTROOT. The aggregate spatial expression of these regulators is not sufficient to predict transcriptional specificity. Instead, modeling, transcriptional reporters, and synthetic promoters support a mechanism whereby expression at the top of the SHORTROOT-SCARECROW cascade is established through opposing activities of activators and repressors. [Display omitted] •A gene-regulatory network reveals regulation of transcription factor expression•Spatially opposed activators and repressors regulate SHORTROOT expression•The top of a transcriptional cascade is regulated by many transcription factors Sparks et al. investigate how tissue-specific expression is established at the top of transcriptional cascades. The authors generated a root-enriched eY1H network to dissect regulation at the top of the SHORTROOT-SCARECROW transcriptional cascade. Their results suggest that SHORTROOT expression is established through the opposing activities of multiple activators and repressors.