AUXIN RESPONSE FACTORS (ARFs) are plant-specific transcription factors (TFs) that couple perception of the hormone auxin to gene expression programs essential to all land plants. As with many large TF families, a key question is whether individual members determine developmental specificity by binding distinct target genes.

We use DAP-seq to generate genome-wide in vitro TF:DNA interaction maps for fourteen maize ARFs from the evolutionarily conserved A and B clades. Comparative analysis reveal a high degree of binding site overlap for ARFs of the same clade, but largely distinct clade A and B binding. Many sites are however co-occupied by ARFs from both clades, suggesting transcriptional coordination for many genes. Among these, we investigate known QTLs and use machine learning to predict the impact of cis-regulatory variation. Overall, large-scale comparative analysis of ARF binding suggests that auxin response specificity may be determined by factors other than individual ARF binding site selection.






 Figure 1: ARF binding events are biologically relevant. a Total number of clade A (orange) and clade B (blue) ARF peaks identified. b Log2 fold enrichment of peaks relative to gene features. Error bars show standard deviation. c ARF peaks are located in putative regulatory regions of known auxin responsive genes. GST-HALO track indicates reads from negative control. Regions of accessible chromatin in immature ears and young leaves as determined by ATAC-seq are depicted as gray bars. Colored bars at bottom correspond to called peaks; orange, clade A ARF; blue, clade B ARF; green, peak called in both clade A and B datasets. d Top motif identified for each ARF. Dendrogram based on ARF amino acid sequence similarity. e Predicted ARF target genes are enriched for functional GO terms related to auxin and other responses.