Fig. 4

Cis-motif enrichment in distinct genic regions is associated with transcription factor (TF) induction or TF repression. TF perturbation assays of the 33 nitrogen (N)-early response TFs in root cells reveals that each TF can act both as an inducer and a repressor of direct target genes (number of targets indicated to the right of TF name). Enrichment analysis revealed that TF cis-binding motifs are often specific to a particular type of regulation (e.g., induction vs. repression). Cis-motif data available for 21/33 TFs enabled us to classify these TFs into four groups. Targets identified by the cell-based TARGET (Transient Assay Reporting Genome-wide Effects of Transcription factors) assay uncovered TFs whose known cis-motifs are associated with induction of targets (group I) and TFs with cis-motifs associated with repression of targets (group II). Another group of TFs (group III), including all the bZIP family members in this study, showed cis-motif enrichment in the promoter or 5’ untranslated region (UTR) of induced targets, while repressed targets only were enriched for the cis-motif in the coding sequence (CDS). The final set of TFs (group IV) showed enrichment of their known cis-motifs in the overlapping regions of both induced and repressed targets. HHO3 and TCP23 showed no enrichment of their cis-motifs in any region and are not shown. One or two representative motifs for each TF from the following sources are shown: DNA affinity purification sequencing (DAP-seq)⁵ with genomic DNA (DAP), DAP-seq with PCR-amplified gDNA (ampDAP), and Cis-BP³⁸ (labeled with motif ID). Orange shading (induced targets) and blue shading (repressed targets) represents the enrichment of motifs as calculated using the AME tool within the MEME suite⁶⁹, with p values determined using Fisher's exact test. Results for all cis-motifs can be found in Supplementary Data 6