Synthetic deconvolution reveals combinatorial properties in transcriptional regulation by auxin

Auxin orchestrates multiple transcriptional programs throughout plant development. In flowering plants, responses to auxin relies on a large multigenic family of transcription factors, the auxin response factors (ARF). While ARF combinations are thought to allow programming specific auxin target gene expression, this hypothesis has not been extensively tested. Here, we used a synthetic-driven reductionist approach to deconvolute the complexity of the ARF-dependent signaling. Synthetic promoters built from cis-elements identified as ARF preferential binding sites allowed us to demonstrate that ARF transcriptional properties are not intrinsic but depend on the cis-elements they bind to. Both in isolated cells and in planta, we show that specificity in transcription is encoded by both combinations of ARFs and of the cis-elements they target. Our results suggest that non-linear interactions between these two control layers constitute a unique regulatory system that can generate a wide diversity of gene expression patterns from the spatial auxin distribution. Overall design: ampDAP-seq experiments with tagged ARF10 proteins were done on 2-weeks old Arabidopsis thaliana seedlings. Affinity purification was perfomed with ARF10 tagged proteins then mixed with DNA. Three replicates were done and only consensus peaks in all three were retained.