The G-box transcriptional regulatory code in Arabidopsis

The G-box (CACGTG) is a DNA element widespread in plant genomes and recognized by two large families of transcription factors (TFs), the basic leucine zipper family (bZIP) and the basic-helix-loop-helix (bHLH) family. Members of these TF families contribute to growth, temperature and light signaling, and drought and immune responses. Collectively there are more than 170 genes encoding members of these two TF families in Arabidopsis. The proteins can bind to their target sequences as homo- or hetero-dimers, which makes matching TFs with their target genes quite complicated. Ezer et al. used in vitro binding and DAP-seq data as well as a large set of RNA-seq time course data to construct a gene regulatory network that identifies the set of bZIPs and bHLHs that are most predictive of expression of genes downstream of perfect G-boxes, and used the network to correctly predict the effects of knocking-out a PIF transcription factor. The Ara-BOX-cis network is available for use by the community. Plant Physiol. 10.1104/pp.17.01086