The G-Box Transcriptional Regulatory Code in Arabidopsis1[OPEN]

• Published in: Plant physiology (Bethesda) 2017-09, Vol.175 (2), p.628-640
• Main Authors: Ezer, Daphne, Shepherd, Samuel J.K., Brestovitsky, Anna, Dickinson, Patrick, Cortijo, Sandra, Charoensawan, Varodom, Box, Mathew S., Biswas, Surojit, Jaeger, Katja E., Wigge, Philip A.
• Format: Article
• Language: English
• Subjects: Breakthrough Technologies
• ISSN: 0032-0889; 1532-2548
• DOI: 10.1104/pp.17.01086

DNA-binding and gene expression data predict which bHLH or bZIP transcription factors are likely regulators of genes near perfect G-box (CACGTG) motifs. Plants have significantly more transcription factor ( TF ) families than animals and fungi, and plant TF families tend to contain more genes; these expansions are linked to adaptation to environmental stressors. Many TF family members bind to similar or identical sequence motifs, such as G-boxes (CACGTG), so it is difficult to predict regulatory relationships. We determined that the flanking sequences near G-boxes help determine in vitro specificity but that this is insufficient to predict the transcription pattern of genes near G-boxes. Therefore, we constructed a gene regulatory network that identifies the set of bZIPs and bHLHs that are most predictive of the expression of genes downstream of perfect G-boxes. This network accurately predicts transcriptional patterns and reconstructs known regulatory subnetworks. Finally, we present Ara-BOX-cis (araboxcis.org), a Web site that provides interactive visualizations of the G-box regulatory network, a useful resource for generating predictions for gene regulatory relations.