Fig. 2

Actively transcribed targets of the master TF regulator bZIP1. a Transcriptomics profile of 4tU-labeled mRNA fractions from cells overexpressing bZIP1 (4tU-bZIP1) and empty vector control (4tU-EV), 5 h after bZIP1 activation. A heat map shows the expression profiles of 115 genes induced and 168 genes repressed by bZIP1 using 4tU-labeling and selection of actively transcribed genes. Heat map shows z-score normalized expression for genes/rows (from light yellow to dark blue gradient) using Mev [29]. Actively induced and repressed bZIP1 targets are ranked according to the number of ACGT hybrid box (0–6 boxes: from blue to red gradient) present in the 1 kb promoter regions upstream of the transcription start site (TSS). Gene ontology (GO) terms over-representation of actively induced and repressed gene sets selected from a singular enrichment analysis using Arabidopsis genome (TAIR10) as a reference with an FDR cutoff of 5 % (also see Additional file 4: Figure S2 for complete GO terms enrichment). b Identification of the known bZIP1 ACGT binding motif based on cis-elements discovery using MEME [32] (top panel, 45 sites, e-value = 6.2e⁻¹¹) and known cis-element enrichment using Elefinder [33] (bottom panel, 299 sites, e-value = 8.2e⁻⁵) using 1 kb promoter regions. The frequency of ACGT hybrid box identified by Elefinder in the 1 kb promoter regions of bZIP1 targets were plotted to show the proximity of binding sites relative to the canonical transcription start site